bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele ages provide limited information about the strength of negative selection
Authors: Shastry Vivaswat , Berg Jeremy J 
Published: December 2024

Abstract
For many problems in population genetics, it is useful to characterize the distribution of fitness effects (DFE) of de novo mutations among a certain class of sites. A DFE is typically estimated by fitting an observed site frequency spectrum (SFS) to an expected SFS given a hypothesized distribution of selection coefficients and demographic history. The development of tools to infer gene trees from haplotype alignments, along with ancient DNA resources, provides us with additional information about the frequency trajectories of segregating mutations. Here, we ask how useful this additional information is for learning about the DFE, using the joint distribution on allele frequency and age to summarize information about the trajectory. To this end, we introduce an accurate and efficient numerical method for computing the density on the age of a segregating variant found at a given sample frequency, given the strength of selection and an arbitrarily complex population size history. We then use this framework to show that the unconditional age distribution of negatively selected alleles is very closely approximated by reweighting the neutral age distribution in terms of the negatively selected SFS, suggesting that allele ages provide little information about the DFE beyond that already contained in the present day frequency. To confirm this prediction, we extended the standard Poisson random field method to incorporate the joint distribution of frequency and age in estimating selection coefficients, and test its performance using simulations. We find that when the full SFS is observed and the true allele ages are known, including ages in the estimation provides only small increases in the accuracy of estimated selection coefficients. However, if only sites with frequencies above a certain threshold are observed, then the true ages can provide substantial information about the selection coefficients, especially when the selection coefficient is large. When ages are estimated from haplotype data using state-of-the-art tools, uncertainty about the age abrogates most of the additional information in the fully observed SFS case, while the neutral prior assumed in these tools when estimating ages induces a downward bias in the case of the thresholded SFS.
The availability of essential medicines in public healthcare facilities in Afghanistan: navigating sociopolitical and geographical challenges
Authors: van Gurp Margo , Alba Sandra , Ammiwala Maida , Arab Sayed Rahim , Sadaat Sayed Murtaza , Hanifi Fazelrabie , Safi Sohrab , Ansari Nasratullah , Campos-Ponce Maiza , Kok Maarten Olivier 
Published: December 2024

Abstract
During the past two decades, the Afghan government, along with the international community, has developed a system aimed at improving access to essential healthcare services under Afghanistan’s challenging sociopolitical and geographical circumstances. In 31 provinces, nonstate actors competed for fixed-term contracts to implement a predefined package of healthcare services. In three provinces, the government organized the provision of healthcare services. An independent third party monitored service provision, including access to medicines. This study examines the availability of essential medicines in Afghanistan’s public healthcare facilities and how this is shaped by sociopolitical challenges, geographical barriers, and the organization of the healthcare system. Between March and July 2021, enumerators collected data at 885 healthcare facilities across Afghanistan. For our analysis, we combined data on medicine availability and the functioning of the health system with publicly available information about geographical and sociopolitical factors, including security incidents. Using regression analysis, we identified facility-, district-, and provincial-level factors related to medicine availability in public healthcare facilities. On average, 70% of 31 selected essential medicines were available in 2021. The availability of medicines varied significantly between provinces and was considerably higher in those where services were contracted out to nonstate actors (n = 31; 91%) compared to provinces where service provision was organized by the government (n = 3; 9%). The most important drivers of variation in medicine availability included geographical barriers, securing and allocating funds at the provincial level, and organizing and sustaining physical capacity at the facility level. Insecurity was not a key factor driving variation in medicine availability. Despite the sociopolitical challenges in 2021, the availability of essential medicines in public healthcare facilities was relatively high. The results suggest that decentralized procurement of medicines by nonstate actors and timely payment of funds contribute to medicine availability. Strategies to improve medicine availability should target hard-to-reach areas and lower-level facilities.
The influence of access to care on the health literacy of families in Mexico
Authors: Hoffman Steven , Ward Kaitlin , Black Alyssa , Kirby Dayna , Wood David S , Marsiglia Flavio F 
Published: December 2024

Abstract
Health literacy (HL) is essential to understanding health information and achieving health goals. Unfortunately, limited information is available on how parent HL impact child health outcomes. This is critical to understand in areas of the world where access to healthcare services is limited or unavailable. Thus, the purpose of this study was to assess the moderating influence of access to care on the relationship between parent HL and child health outcomes in Mexico. Using a geographically stratified convenience sample survey design, we gathered a sample of 373 parent–child dyads throughout Mexico in August of 2021. Using the HLS-Q12, the Warwick-Edinburgh Mental Wellbeing Scale, healthcare access questions developed by Levy and Janke, a single-item self-report overall health measure, and questions about substance use frequency, we found that parent HL was positively associated with youth mental wellbeing and overall health. Limited healthcare access was associated with increased youth cigarette, marijuana and alcohol use. Our results indicate that efforts to increase parent HL may be effective in improving youth health behaviors and outcomes.
Domestication history and genetic changes for the newly evolved flower color in the ornamental plant Lobularia maritima (Brassiaceae)
Authors: Yang Wenjie , Liu Meng , Feng Landi , Jiao Pengfei , Jiang Jiebei , Huang Li , Liu Jianquan , Lopez-Pujol Jordi , Hu Quanjun 
Published: December 2024

Abstract
Lobularia maritima (sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a de novo assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic and wild representatives. These analyses revealed distinct genetic clusters corresponding to wild and domestic groups, with further subdivisions based on geographic and phenotypic differences. Importantly, all cultivars originated from a single domestication event within the Tunisia group. One wild group did not contribute genetically to the current cultivars. The new mutations in key gene of the anthocyanin biosynthetic pathway, PAP1, that arose following domestication led to the origin of purple flower coloration in the cultivars. Moreover, the contrasting PAP1 haplotypes in white and purple varieties lead to differential expression of CHS and DFR, which in turn contributes to the observed flower color differences. These findings provide key insights into the domestication history and genetic regulation of flower color in L. maritima, laying the groundwork for future genetic breeding efforts focused on this plant, especially introducing genetic sources from other wild groups.
Low Surgery Rates in Early Crohn’s Disease: Results from a Prospective Population-Based Inception Cohort—The Inflammatory Bowel Disease in South-Eastern Norway III Study
Authors: Lund Charlotte , Strande Vibeke , Hagen Milada , Bengtson May-Bente , Boyar Raziye , Detlie Trond Espen , Frigstad Svein Oskar , Medhus Asle W , Henriksen Magne , Holten Kristina I Aass , Hovde Øistein , Huppertz-Hauss Gert , Johansen Ingunn , Olsen Bjørn Christian , Opheim Randi , Pallenschat Jens , Perminow Gøri , Ricanek Petr , Torp Roald , Ystrøm Carl Magnus , Høie Ole , Asak Øivind , Vatn Simen , Aabrekk Tone Bergene , Kristensen Vendel A , Høivik Marte Lie 
Published: December 2024

Abstract

Background and Aims
The emergence of biologic therapy has coincided with a decline in surgery rates for Crohn’s disease (CD). This study aims to describe the disease course, including intra-abdominal surgery rates, biologic therapy use, and variables associated with biologic therapy initiation in a cohort of newly diagnosed CD patients.

Methods
The Inflammatory Bowel Disease in South-Eastern Norway (IBSEN) III study is a population-based inception cohort study. From 2017 to 2019, newly diagnosed inflammatory bowel disease patients were included for prospective follow-up. The present study included CD patients ≥ 18 years. Clinical, endoscopic, and demographic data were collected at diagnosis and 1-year follow-up. Data were analyzed by using the Kaplan–Meier method and regression analyses.

Results
In total, 424 CD patients (median age 37.0 years (range 18-80), female 55.0%) were included. At diagnosis, 50.5% presented with ileal disease and 80.7% with inflammatory behavior. Within a 1-year follow-up, 39.6% of patients received their first biologic therapy and 5.2% required intra-abdominal surgery. Systemic steroid treatment, CRP ≥ 5.0 mg dL−1, Harvey–Bradshaw Index score &gt; 4, ileocolonic disease and penetrating disease behavior at diagnosis were independently associated with increased risk of initiation of biologic therapy, while age &gt; 40 years was associated with decreased risk.

Conclusion
A high proportion of patients had ileal disease and inflammatory behavior at diagnosis. Still, nearly 40% started biologic therapy within the 1-year follow-up, while only 5% required intra-abdominal surgery.
A practical identification guide to the zoeae of the invasive European green crab, Carcinus maenas (Linnaeus, 1758) (Decapoda: Brachyura: Carcinidae), and to the zoeae of the families of brachyuran crabs in Washington state, USA
Authors: Burnett Nicole 
Published: December 2024

Abstract
Although the brachyuran crab Carcinus maenas (Linnaeus, 1758) is a globally invasive species, early-life history information for its larvae, such as hatch timing, stage duration, dispersal, and behavior, is limited, particularly in newly invaded locations. This is, in part, due to the need for region-specific guides on larval taxonomy that incorporate C. maenas. We addressed this issue for Washington state marine waters by developing a dichotomous key for the zoeae of C. maenas and a matrix that compares the morphological characters of C. maenas zoeae to those of brachyuran crab families reported from the state. To assess whether morphological characters of C. maenas from this region reflect taxonomic descriptions from the species’ native range, we reared zoeae from females collected in Washington state. We found that zoeae from each crab family reported from Washington state have at least two characters that distinguish them from C. maenas zoeae: the presence of lateral carapace spines in most of these families, and for three families lacking lateral carapace spines (Epialtidae, Grapsidae, Pinnotheridae) antennae that are nearly equal to the length of the rostral spine, the presence of posterolateral extensions on any of the somites, or a laterally expanded last somite, respectively. Rearing of larvae showed that the rostral spines of the Washington zoeae I of C. maenas were ~ 0.06 mm longer than reported in the literature. We also found that late-stage zoeae may retain more furcal spines than previously reported. The region-specific taxonomic tools we developed allow easier and quicker identification of C. maenas zoeae in Washington. These descriptions should facilitate early detection in newly invaded bays, a more rapid understanding of C. maenas larval timing and behavior, and better evaluation of larval dispersal that can be used in risk-assessment tools.
FX Comovements and Their Economic Determinants
Authors: Rangel Jose Gonzalo 
Published: December 2024

Abstract
This article models high- and low-frequency dynamic components of FX excess return correlations and examines their relationship with economic fundamentals. A factor pricing model with time-varying betas is used to characterize these correlations. From the low-frequency components, an aggregate comovement measure is derived. This component is countercyclical relative to the U.S., as it is negatively related to economic growth and positively related to both inflation volatility and economic policy uncertainty. Idiosyncratic volatilities also drive currency comovements. I examine their cross-sectional variation and find significant impacts of inflation levels, monetary policy variables, real output growth, trade, and capital flows.
Socioeconomic determinants of cancer screening adherence among cancer survivors: analysis from the 2020 Behavioral Risk Factor Surveillance System
Authors: Beatrici Edoardo , Qian Zhiyu , Filipas Dejan K , Stone Benjamin V , Dagnino Filippo , Labban Muhieddine , Lipsitz Stuart R , Lughezzani Giovanni , Buffi Nicolò M , Cole Alexander P , Trinh Quoc-Dien 
Published: December 2024

Abstract

Background
Factors associated with cancer survivors’ preventive health behaviors are understudied. We hypothesized that socioeconomic and health-care access factors may be associated with adherence to recommended cancer screenings.

Methods
We conducted a cross-sectional analysis using the 2020 Behavioral Risk Factor Surveillance System. Cancer survivors eligible for United States Preventive Services Task Force–recommended breast, cervical, prostate, and colorectal screenings were included. Multivariable logistic regression models were used to identify socioeconomic factors significantly associated with screening adherence.

Results
Overall, 64 958 (weighted national estimate = 29 066 143) cancer survivors were included. Adherence rates varied across cancer types: 80.9% for breast, 88.9% for cervical, 54.1% for prostate, and 84.7% for colorectal cancer. Key predictors of low adherence included lower income (breast: adjusted odds ratio [aOR] = 0.56, 95% confidence interval [CI] = 0.43 to 0.74; cervical: aOR = 0.38, 95% CI = 0.24 to 0.59; prostate: aOR = 0.36, 95% CI = 0.24 to 0.52; colorectal: aOR = 0.74, 95% CI = 0.57 to 0.96), lack of health-care coverage for colorectal cancer (aOR = 0.51, 95% CI = 0.36 to 0.73), time since last checkup between 1 and 2 years prior for breast (aOR = 0.58, 95% CI = 0.45 to 0.75), prostate (aOR = 0.66, 95% CI = 0.47 to 0.91), and colorectal (aOR = 0.69, 95% CI = 0.56 to 0.86) cancer, and no health-care provider for breast (aOR = 0.68, 95% CI = 0.47 to 0.98), prostate (aOR = 0.45, 95% CI = 0.31 to 0.65), and colorectal (aOR = 0.51, 95% CI = 0.40 to 0.66) cancer.

Conclusion
Cancer survivors’ adherence to screening is associated with factors including lack of health-care coverage, lower income, time since the last exam, and having a personal provider. Targeted interventions accounting for such factors may help mitigate these disparities.
Conjoined partners: efficacy and side effects of grafting and dsRNA application on the microbial endophyte population of grapevine plants inoculated with two esca-related fungal pathogens
Authors: Nerva Luca , Gambino Giorgio , Moffa Loredana , Spada Alberto , Falginella Luigi , De Luca Elisa , Zambon Yuri , Chitarra Walter 
Published: December 2024

Abstract
Grafting has been exploited since 7000 BC to enhance productivity, disease resistance, and adaptability of cultivated plants to stressful conditions especially in woody crops such as grapevine (Vitis spp.). In contrast, the application of sequence specific double-stranded RNAs (dsRNAs) to control fungal pathogens and insect pests has only been recently developed. The possibility of combining these approaches to enhance plant resilience, reducing reliance on pesticides, offers new perspectives for a more sustainable agriculture. In this study, we assessed the potential of utilizing dsRNAs to enhance resilience against esca-related wood fungal pathogens in grapevine, considering various rootstock–scion combinations. The results showed that the scion genotype modulates the ability of the rootstock to cope with the inoculated wood fungal pathogens, mainly by altering the efficacy of producing stilbene compounds. Additionally, we found that dsRNAs reduced the growth of two inoculated esca-related fungal pathogens but they did not completely stop their colonization. Furthermore, wood microbiome data showed that the scion genotype (always belonging to Vitis vinifera species) was also able to influence the rootstock-associated microbiota, with a major effect on the fungal community. Lastly, adverse effects on non-target microorganisms are reported, raising questions on the environmental fate of dsRNAs and how dsRNAs can directly or indirectly affect plant-associated microbial communities.
The maize aquaporin ZmPIP1;6 enhances stomatal opening and CO2- and ABA-induced stomatal closure
Authors: Ding Lei , Laurent Maxime J , Milhiet Thomas , Aesaert Stijn , Van Lijsbettens Mieke , Pauwels Laurens , Nelissen Hilde , Inzé Dirk , Chaumont François 
Published: December 2024

Abstract
The plasma membrane aquaporin ZmPIP1;6 is expressed in maize stomatal complexes, with higher expression during the day than at night. To elucidate the role of ZmPIP1;6 in gas exchange and stomatal movement, it was expressed in maize (inbred line B104) under the control of the p35S promoter (overexpression) or its native promoter fused with mYFP (monomeric yellow fluorescent protein) cDNA (mYFP-ZmPIP1;6). In stomatal complexes of the mature zone of the leaf, mYFP–ZmPIP1;6 showed higher expression in subsidiary cells than in guard cells, and light and dark treatments influenced its subcellular localization. Notably, ZmPIP1;6 internalization increased in dark conditions compared with light. Stomatal opening was greater in ZmPIP1;6 overexpression plants than in the wild type, while closure exhibited greater sensitivity to elevated CO2 concentration or abscisic acid (ABA) treatment. Our findings revealed that reactive oxygen species (H2O2) were involved in ABA-induced stomatal closure, while ZmPIP1;6 was unable to facilitate H2O2 diffusion when expressed in yeast. Finally, ZmPIP1;6 overexpression and mYFP-ZmPIP1;6 transgenic plants exhibited higher abaxial stomatal density than the wild type. Overall, these results indicate that ZmPIP1;6 plays important roles in stomatal opening and CO2- and ABA-induced stomatal closure.
Cracking the code of aldosterone synthase deficiency: bridging genetics and biochemistry: a case report
Authors: Kamarajan Lekha Priyadharshini , Mahto Mala , Kumar Sushil , Kumar Pradeep 
Published: December 2024

Abstract

Objective
Aldosterone synthase deficiency (ASD) is a rare autosomal recessive inherited disease with an overall clinical phenotype of failure to thrive, vomiting, severe dehydration, hyperkalemia, and hyponatremia. Mutations in the CYP11B2 gene encoding AS are responsible for the occurrence of ASD. Defects in CYP11B2 gene have only been reported in a limited number of cases worldwide. Due to this potential life-threatening risk, a comprehensive hormonal investigation followed by genetic confirmation is essential for the clinical management of offspring.

Methods
We report a case of a newborn who was found to have persistent hyponatremia, hyperkalemia, low aldosterone level, raised renin levels, normal cortisol, and normal 17 hydroxyprogesterone level, suggesting the diagnosis of isolated ASD.

Results
Genetic report was suggestive of isolated ASD caused by a novel base pair deletion in exon 3, homozygous CYP11B2 variant (chr8:g.142915123_142915125del; depth: 124x d) (p.Lys175del; ENST00000323110.2). After initial steps of rehydration and salt restoration, the child was started on oral tablet fludrocortisone. The child responded well and showed a good gain in growth and development.

Discussion
We elaborate on the biochemical and genetic work-up performed and describe potential pitfalls in CYP11B2 sequencing due to its homology to CYP11B1.
Updates in Human Papillomavirus Vaccination to Improve Medical Readiness in Active Duty Service Members
Authors: Hope Erica R , Kopelman Zachary A , Darcy Kathleen M , Penick Emily R 
Published: December 2024

ABSTRACT
Human papillomavirus (HPV) is the most common sexually transmitted infection in the United States and is associated with the development of genital warts, precancerous lesions, and cancers of the oropharynx, anus, penis, vulva, vagina, and cervix. HPV-associated diseases are preventable through vaccination. An Australian nationwide vaccination program will effectively eliminate cervical cancer as a public health concern by the year 2035. Despite safety and efficacy data, vaccination against HPV is not mandatory for military service members. Active duty service women are more likely to test positive for HPV when compared to dependents, and veterans diagnosed with HPV-associated cancers have higher health care resource utilization and costs. Even if a patient has a prior HPV infection, vaccination at the time of HPV diagnosis or following treatment can reduce recurrence of HPV and dysplasia. In addition, patients with a history of cancer have a higher incidence of secondary HPV-associated malignancies and should be offered vaccination or re-vaccination if they received a hematopoietic stem-cell transplant. Improving HPV vaccination rates within the military health system requires a multidisciplinary approach. Providers should use every opportunity to recommend HPV vaccination, including recommending HPV vaccines for individuals who do not have a record of HPV vaccination. The electronic health record can be utilized to generate prompts for vaccine reminders, and clinics should stock HPV vaccines to allow for easy administration. Additionally, adoption of an opt-out policy for HPV vaccines rather than mandatory vaccination may be an acceptable alternative to increase HPV vaccination while allowing active duty service members to retain autonomy.