Miracle-dz/UniFAR-FTUs huggingface dataset:
Proxy use of patient portals on behalf of children: Federally Qualified Health Centers as a case study

Objective This study examined the proxy use of patient portals for children in a large Federally Qualified Health Centers (FQHC) network in Texas. Methods We used de-identified individual-level data of patients, 0–18 years, who had 1+ visits between December 2018 and November 2020. Logistic regression was used to examine patient-, clinic-, and geographic-level factors associated with portal usage by an assumed proxy (i.e. parent or guardian). Results The proxy portal usage rate increased from 28% in the pre-pandemic months (November 2018–February 2020) to 34% in the pandemic months (March–Nov 2020). Compared to patients 0–5 years, patients aged 6 to 18 years had lower odds of portal usage (6–10 OR: 0.77, p < 0.001; 11–14 OR: 0.62, p < 0.001; 15–18 OR: 0.51, p < 0.001). Minoritized groups had significantly lower odds of portal usage when compared to their non-Hispanic White counterparts (non-Hispanic Black OR: 0.78, p < 0.001; Hispanic OR 0.63, p < 0.001; Asian OR: 0.69, p < 0.001). Having one chronic condition was associated with portal usage (OR: 1.57, p < 0.001); however, there were no significant differences in portal usage between those with none or multiple chronic conditions. Portal usage also varied by service lines, with obstetrics and gynecology (OR: 1.84, p < 0.001) and behavioral health (OR 1.82, p < 0.001) having the highest odds of usage when compared to pediatrics. Having a telemedicine visit was the strongest predictor of portal usage (OR: 2.30, p < 0.001), while residence in zip codes with poor broadband internet access was associated with lower odds of portal usage (OR: 0.97, p < 0.001). Conclusion While others have reported portal usage rates as high as 64% in pediatric settings, our analysis suggests proxy portal usage rates of 30% in pediatric FQHC settings, with race/ethnicity, age group, and chronic disease status being significant drivers of portal non-usage. These findings highlight the need for appropriate and responsive health information technology approaches for vulnerable populations receiving care in low-resource settings.
Lower constraint testing enhances the testing effect for some contextual details but not others

Abstract Introduction Retrieval practice has been shown to be an effective means of learning new information, a memory phenomenon known as the testing effect or the retrieval practice effect. Some work suggests that the magnitude of the testing effect can be enhanced when the test used for retrieval practice uses fewer cues to retrieve previously studied information. It is unclear, however, whether such testing benefits extend to peripheral contextual details associated with studied materials (e.g., location where stimuli appear, font color in which items are presented, etc.). In this experiment, we examine both item memory (i.e., memory for the studied items) and context memory under conditions where the intervening test offers fewer cues (i.e., lower constraint) compared to more cues (higher constraint) to better understand item and context memory testing effects. Methods Participants first studied word pairs presented in one of eight locations as well as in either red or green font color. Then, in the re‐exposure phase, participants processed materials in two types of intervening tests (lower constraint and a higher constraint test) as well as in a restudy condition, before a final memory test. Results For item memory, results showed that memory was better in the lower constraint testing condition compared to both the higher constraint testing condition as well as the restudy (control) condition. For context memory, results indicated improved memory for location context under lower constraint testing compared to both higher constraint testing and restudy conditions. There was no difference in memory, however, for color context across all conditions. Conclusion Overall, these findings suggest that providing fewer cues to aid retrieval in the intervening test can induce better memory for both items as well as some contextual details.
Genome-Wide Identiﬁcation and Expression Proﬁling of Heavy Metal ATPase (HMA) Genes in Peanut: Potential Roles in Heavy Metal Transport

: The heavy metal ATPase (HMA) family belongs to the P-type ATPase superfamily and plays an essential role in the regulation of metal homeostasis in plants. However, the gene family has not been fully investigated in peanut. Here, a genome-wide identiﬁcation and bioinformatics analysis was performed on AhHMA genes in peanut, and the expression of 12 AhHMA genes in response to Cu, Zn, and Cd was evaluated in two peanut cultivars (Silihong and Fenghua 1) differing in Cd accumulation. A total of 21 AhHMA genes were identiﬁed in the peanut genome, including ten paralogous gene pairs derived from whole-genome duplication, and an additional gene resulting from tandem duplication. AhHMA proteins could be divided into six groups (I–VI), belonging to two clades (Zn/Co/Cd/Pb-ATPases and Cu/Ag-ATPases). Most AhHMA proteins within the same clade or group generally have a similar structure. However, signiﬁcant divergence exists in the exon/intron organization even between duplicated gene pairs. RNA-seq data showed that most AhHMA genes are preferentially expressed in roots, shoots, and reproductive tissues. qRT-PCR results revealed that AhHMA1.1 / 1.2 , AhHMA3.1 / 3.2 , AhHMA7.1 / 7.4 , and AhHMA8.1 might be involved in Zn transport in peanut plants, while AhHMA3.2 and AhHMA7.5 might be involved in Cd transport. Our ﬁndings provide clues to further characterize the functions of AhHMA genes in metal uptake and translocation in peanut plants.
Trumpism, climate and COVID: Social bases of the new science rejection

Although the hazards posed by greenhouse warming and COVID-19 are quite different, diagnosis and mitigation prospects for both depend heavily on science. Unfortunately, the reality of both threats has been subject to politicized science rejection in the US, making these deadly problems less tractable. There are substantial parallels between the two cases of science rejection, including common rhetoric and conservative political leadership. Survey research has reached widely-replicated conclusions regarding the social bases of climate-change perceptions. Corresponding studies of COVID-19 perceptions have found some political commonalities, but less agreement on other details. Here, we address this gap using generalized structural equation modeling (GSEM) and 2021 US survey data to make direct comparisons between the social bases of rejecting the reality of anthropogenic climate change (ACC) and rejecting COVID-19 vaccination. Trumpism, operationalized from approval of ex-president Trump, is viewed as an intervening variable that influences both types of science rejection. Trumpism itself is predicted by age, race, evangelical religion, ideology, and receptivity to seemingly non-political conspiracy beliefs. Considering direct as well as indirect effects (through Trumpism), climate change and vaccine rejection are similarly predicted by white and evangelical identity, conspiracism, and by education×ideology and friends×party interactions. The finding that Trumpism exacerbates science rejection could also apply to other science- and expertise-related topics unrelated to climate and COVID. These results invite broader comparisons across topics, with analogous movements in other countries, and continued tracking as US Trumpism evolves beyond Trump.
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

Abstract There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet. org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user’s applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet. org/.
Transmission of fluoroquinolones resistance among multidrug-resistant tuberculosis in Shanghai, China: a retrospective population-based genomic epidemiology study

ABSTRACT Fluoroquinolones (FQ) are essential for the treatment of multidrug-resistant tuberculosis (MDR-TB). The FQ resistance (FQ-R) rate in MDR-TB in China and its risk factors remain poorly understood. We conducted a retrospective, population-based genomic epidemiology study of MDR-TB patients in Shanghai, China, from 2009 to 2018. A genomic cluster was defined as strains with genetic distances ≤ 12 single nucleotide polymorphisms. The transmitted FQ-R was defined as the same FQ resistance-conferring mutations shared by ≥ 2 strains in a genomic cluster. We used multivariable logistic regression analysis to identify the risk factors for drug resistance. Among the total 850 MDR-TB patients included in the study, 72.8% (619/850) were male, the median age was 39 (interquartile range 28, 55) years, 52.7% (448/850) were migrants, and 34.5% (293/850) were previously treated patients. Most of the MDR-TB strains belong to the Beijing lineage (91.7%, 779/850). Overall, the genotypic resistance rate of FQ was 34.7% (295/850), and 47.1% (139/295) FQ-R patients were in genomic clusters, of which 98 (33.2%, 98/295) were presumed as transmitted FQ-R. Patients with treatment-naïve (aOR = 1.84; 95% CI: 1.09, 3.16), diagnosed in a district-level hospital (aOR = 2.69; 95% CI: 1.56, 4.75), and streptomycin resistance (aOR = 3.69; 95% CI: 1.65, 9.42) were significantly associated with the transmission of FQ-R. In summary, the prevalence of FQ-R among MDR-TB patients was high in Shanghai, and at least one-third were transmitted. Enforced interventions including surveillance of FQ drug susceptibility testing and screening among MDR-TB before initiation of treatment were urgently needed.
Educational outcomes in siblings of childhood leukemia survivors: Factors associated with school difficulties and comparison with general population

Abstract Background To investigate the educational outcomes of siblings of childhood leukemia survivors, explore determinants of school difficulties, and compare the rates of repeating grades between siblings and the general population. Methods A cross‐sectional study of childhood leukemia survivors' siblings recruited through the Leucémies de l'Enfant et de l'Adolescent cohort, a French long‐term follow‐up program, was conducted, and education‐related data were obtained via self‐report questionnaires. Adjusted logistic regression models were used to identify variables associated with school difficulties and time since diagnosis. Rates of repeating a grade in middle school were compared between siblings and the general population of the same generation. Results A total of 564 siblings with a mean time from diagnosis of 14.1 ± 6.4 years were included, among whom 139 (24.6%) repeated a grade, at an average of 6.4 ± 4.5 years after diagnosis. In multivariate analysis, the risk factors for repeating a grade were older siblings (odds ratio [OR] 2.3, p = 0.006), family financial difficulties (OR 2.8, p = 0.008), and history of repetition in survivors (OR, 2.5, p = 0.001). Sibling hematopoietic stem cell donors were at greater risk of repeating a grade long‐term after diagnosis (p = 0.018). Overall, siblings did not have a higher risk of educational delays at the end of middle school than the general population. Conclusion Although the results are reassuring, socioeconomic and cancer‐related factors may have an impact on siblings' schooling long after diagnosis. Paying attention to siblings contributes to identifying the most vulnerable families, allowing more attention and appropriate resources to avoid long‐term repercussions. Additionally, supportive and targeted interventions can be developed to improve the organization of education and the health care system.
Red cabbage juice-mediated gut microbiota modulation improves intestinal epithelial homeostasis and ameliorates colitis

Gut microbiota plays a crucial role in inflammatory bowel disease (IBD) and has therapeutic benefits. Thus, targeting the gut microbiota is a promising therapeutic approach for IBD treatment. We recently found that red cabbage juice (RCJ) ameliorates dextran sulfate sodium (DSS)-induced colitis in mice. However, the underlying mechanisms remain unknown. The current study investigated the modulation of gut microbiota in response to treatment with RCJ to ameliorate the DSS colitis. The initial results demonstrated that mice treated with DSS + RCJ showed increased body weight and decreased diarrhea and blood in feces compared to the DSS alone group. RCJ ameliorated colitis by regulating the intestinal barrier function by reducing the number of apoptotic cells, improving colonic protective mucin, and increasing tight junction protein in RCJ + DSS groups compared to the DSS group. Short-gun metagenomic analysis revealed significant enrichment of short-chain fatty acid (SCFAs)-producing bacteria (Butyrivibrio, Ruminococcaceae, Acetatifactor muris, Rosburia Sp. CAG:303, Dorea Sp. 5-2) increased PPAR-© activation, leading to repression of the nuclear factor κB (NFκB) signaling pathway, thus decreasing the production of crucial inflammatory cytokines and chemokines in the RCJ + DSS groups compared to the DSS group. Pathway abundance analysis showed an increased abundance of the SCFA pathway, reduced histidine degradation (Bacteroides sartorii, and Bacteroides caecimuris), and LCFA production in the RCJ+DSS treated group, suggesting the promotion of good colonic health. Furthermore, increased T-reg (FOXP3+) cells in the colon were due to SCFAs produced by the gut microbiota, which was corroborated by an increase in IL-10, a vital anti-inflammatory cytokine. Thus, our study provides the first evidence that RCJ ameliorates colonic inflammation by modulating the gut microbiota.
Syntrophic microbes involved in the oxidation of short-chain fatty acids in continuous-flow anaerobic digesters treating waste activated sludge with hydrochar

ABSTRACT The rapid degradation of short-chain fatty acids (SCFAs) is an essential issue of anaerobic digestion (AD), in which SCFA oxidizers could generally metabolize in syntrophy with methanogens. The dynamic responses of active metagenome-assembled genomes to low concentrations of propionate and acetate were analyzed to identify specific syntrophic SCFA oxidizers and their metabolic characteristics in continuous-flow AD systems treating waste activated sludge with and without hydrochar. In this study, hydrochar increased methane production by 19%, possibly due to hydrochar enhancing acidification and methanogenesis processes. A putative syntrophic propionate oxidizer and two acetate oxidizers contributed substantially to the syntrophic degradation of SCFAs, and hydrochar positively regulated their functional gene expressions. A significant relationship was established between the replication rate of SCFA oxidizers and their stimulation-related transcriptional activity. Acetate was degraded in the hydrochar group, which might be mainly through the syntrophic acetate oxidizer from the genus Desulfallas and methanogens from the genus Methanosarcina. IMPORTANCE Short-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar. Short-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar.
Human alveolar echinococcosis in Slovakia: Epidemiology and genetic diversity of Echinococcus multilocularis, 2000–2023

Human alveolar echinococcosis (AE) is a serious parasitic disease caused by larval stages of Echinococcus multilocularis. Between January 2000 and October 2023, 137 AE cases were confirmed in Slovakia. The average annual incidence increased from 0.031 per 100,000 inhabitants between 2000 and 2011, to an average of 0.187 since 2012, i.e. about six times. Among patients, 45.3% were men and 54.7% were women; the mean age at the time of diagnosis was 52.8 years. Most cases were diagnosed in the age groups 51–60 years and 61–70 years (33 cases each), and eight patients fell into the age category ≤ 20 years. To better recognize the gene diversity in clinical samples, metacestodes from 21 patients collected between 2013 and 2021 were subjected to DNA sequencing of four mitochondrial genes. Using concatenated sequences of cob (603 bp), nad2 (882 bp) and cox1 (789 bp) gene fragments, 14 isolates (66.7%) were assigned to the European E5 profile of E. multilocularis, two isolates (9.5%) to the E5a subtype, four isolates (19%) to the E4 profile, and one isolate (4.8%) to haplogroup E1/E2. The E5-type profiles and E4 profiles were distributed throughout the country, whereas the E1/E2 profile was found in the patient from western Slovakia. According to the data obtained and GenBank sequences, the E5-type dispersal is so far limited to central-eastern Europe and the variant seems to be indigenous to that region. The admixture with the haplotypes E4 and E1/E2 could have taken place from a historical endemic focus during the fox expansion in the last decades. By employing the nad1 fragment, a typical European haplotype was observed in all 21 resolved Slovak samples. The acceleration in the AE incidence in the last decade suggests the emergence of the disease and the need for further research on human and animal isolates.
Home range and spawning migration patterns of queen triggerfish Balistes vetula in St. Croix, US Virgin Islands

Queen triggerfish Balistes vetula are an ecologically and economically important species associated with coral reefs throughout the tropical Atlantic Ocean. To better understand spatial and temporal movement patterns and help determine the effectiveness of a no-take marine reserve (Buck Island Reef National Monument, BIRNM), 55 queen triggerfish were surgically implanted with acoustic transmitters and tracked for 434.6 ± 27.3 d (mean ± SE) within a large acoustic array in St. Croix, US Virgin Islands. Queen triggerfish displayed high site fidelity within the reserve during non-spawning months. Home range sizes, as measured by 95% minimum convex polygons and kernel utilization distributions, averaged 2.44 ± 0.30 and 3.34 ± 0.17 km2, respectively. High site fidelity was interrupted briefly during full moons from November to March (2015–2017), when 22% of the tagged population (n = 12) undertook repeated migrations to a nesting area located approximately 12 km from BIRNM. During the same-season spawning periods, 5 other fish were exclusively detected at a receiver station within the reserve, indicating a possible local nesting area and resident (non-migratory) contingent of queen triggerfish. The high site fidelity of queen triggerfish during non-spawning months coupled with the discovery of a resident spawning population highlights the importance of BIRNM as a potential refuge from local fishing pressures. This study provides improved understanding of queen triggerfish movement ecology, an extremely valuable asset for the development of spatial management strategies throughout their range.
Health care–related transportation insecurity is associated with adverse health outcomes among adults with chronic liver disease

Background: Health care–related transportation insecurity (delayed or forgone medical care due to transportation barriers) is being increasingly recognized as a social risk factor affecting health outcomes. We estimated the national burden and adverse outcomes of health care–related transportation insecurity among US adults with chronic liver disease (CLD). Methods: Using the U.S. National Health Interview Survey from 2014 to 2018, we identified adults with self-reported CLD. We used complex weighted survey analysis to obtain national estimates of health care–related transportation insecurity. We examined the associations between health care–related transportation insecurity and health care–related financial insecurity, food insecurity, self-reported health status, work productivity, health care use, and mortality. Results: Of the 3643 (representing 5.2 million) US adults with CLD, 267 [representing 307,628 (6%; 95% CI: 5%–7%)] reported health care–related transportation insecurity. Adults with CLD experiencing health care–related transportation insecurity had 3.5 times higher odds of cost-related medication nonadherence [aOR, 3.5; (2.4–5.0)], 3.5 times higher odds of food insecurity [aOR, 3.5; (2.4–5.3)], 2.5 times higher odds of worsening self-reported health status over the past year [aOR, 2.5; (1.7–3.7)], 3.1 times higher odds of being unable to work due to poor health over the past year [aOR, 3.1; (2.0–4.9)], and 1.7 times higher odds of being in a higher-risk category group for number of hospitalizations annually [aOR, 1.7; (1.2–2.5)]. Health care–related transportation insecurity was independently associated with mortality after controlling for age, income, insurance status, comorbidity burden, financial insecurity, and food insecurity [aHR, 1.7; (1.4–2.0)]. Conclusions: Health care–related transportation insecurity is a critical social risk factor that is associated with health care–related financial insecurity, food insecurity, poorer self-reported health status and work productivity, and increased health care use and mortality among US adults with CLD. Efforts to screen for and reduce health care–related transportation insecurity are warranted.