bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow)
Authors: Wade Miranda J , Bucci Kennedy , Rochman Chelsea M , Meek Mariah H 
Published: May 2024

Abstract
Microplastics have evolutionary and ecological impacts across species, affecting organisms’ development, reproduction, and behavior along with contributing to genotoxicity and stress. As plastic pollution is increasing and ubiquitous, gaining a better understanding of organismal responses to microplastics is necessary. Epigenetic processes such as DNA methylation are heritable forms of molecular regulation influenced by environmental conditions. Therefore, determining such epigenetic responses to microplastics will reveal potential chronic consequences of this environmental pollutant. We performed an experiment across two generations of fathead minnows (Pimephales promelas) to elucidate the transgenerational epigenetic effects of microplastic exposure. We exposed the first generation of fish to four different treatments of microplastics: two concentrations of each of pre-consumer polyethylene (PE) and PE collected from Lake Ontario. We then raised the first filial generation with no microplastic exposure. We used enzymatic methylation sequencing on adult liver tissue and homogenized larvae to evaluate DNA methylation differences among treatments, sexes, and generations. Our findings show the origin of the plastic had a larger effect in female minnows whereas the effect of concentration was stronger in the males. We also observed transgenerational effects, highlighting a mechanism in which parents can pass on the effects of microplastic exposure to their offspring. Many of the genes found within differentially methylated regions in our analyses are known to interact with estrogenic chemicals associated with plastic and are related to metabolism. This study highlights the persistent and potentially serious impacts of microplastic pollution on gene regulation in freshwater systems.
Military Family Perspectives on Enrollment and Engagement in the WIC Program
Authors: Chokshi Binny , Zven Sidney , Burris Rachel , Wido Meaghan , Hisle-Gorman Elizabeth 
Published: May 2024

ABSTRACT

Introduction
One in four U.S. service members endorses food insecurity. The Supplemental Nutrition Program for Women, Infants, and Children (WIC) is an invaluable, underutilized resource that can increase access to nutritious food for families with children under 5 years of age. Our research sought to evaluate military family perceptions and engagement with the WIC program.

Materials and Methods
We conducted a mixed-method study, recruiting from a convenience sample of military families who applied for financial assistance for child care. An 18-question survey and follow-up focus groups assessed participant demographics and experiences with WIC. We utilized descriptive statistics ordinal logistic regression analyses for quantitative data analysis. For qualitative data, descriptive content analysis with constant comparison and inductive and deductive coding of interviews identified emerging themes. This study was approved by the Uniformed Services University of the Health Sciences Institutional Review Board.

Results
Among the 399 survey respondents, 25% were currently enrolled in WIC and 39% had been previously enrolled. Service members and their partners learned about WIC from a variety of sources, and there was no significant association between the branch of service or rank and WIC enrollment. There were 40 total participants in 10 completed focus groups. Six themes emerged: (1) Military-specific factors create unique circumstances related to WIC engagement; (2) the WIC program facilitates access to formula supplementation and nutritious foods for military families; (3) lack of program awareness and misinformation are top barriers to WIC engagement in military families; (4) stigma impacts WIC program enrollment and engagement; (5) logistics of enrollment can impact WIC engagement among military families; and (6) the military can support WIC enrollment and engagement through standardization, education, and leadership commitment.

Conclusions
Our findings suggest that unique circumstances related to military family life create a profound need for programs addressing food support, such as WIC. Interventions to improve WIC enrollment among military families need to be rooted in broad outreach efforts, not targeted at specific ranks, branches, or ages. Specific recommendations include increasing information dissemination, universally screening military families for WIC, decreasing logistical burdens, and involving military leadership.
Structural basis for double-stranded RNA recognition by SID1
Authors: Wang Runhao , Cong Ye , Qian Dandan , Yan Chuangye , Gong Deshun 
Published: May 2024

Abstract
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2′-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction
Authors: Bernard Clément , Postic Guillaume , Ghannay Sahar , Tahi Fariza 
Published: May 2024

Abstract
RNAs are essential molecules involved in numerous biological functions. Understanding RNA functions requires the knowledge of their 3D structures. Computational methods have been developed for over two decades to predict the 3D conformations from RNA sequences. These computational methods have been widely used and are usually categorised as either ab initio or template-based. The performances remain to be improved. Recently, the rise of deep learning has changed the sight of novel approaches. Deep learning methods are promising, but their adaptation to RNA 3D structure prediction remains difficult. In this paper, we give a brief review of the ab initio, template-based and novel deep learning approaches. We highlight the different available tools and provide a benchmark on nine methods using the RNA-Puzzles dataset. We provide an online dashboard that shows the predictions made by benchmarked methods, freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/state_of_the_rnart/.
MUFFIN: a suite of tools for the analysis of functional sequencing data
Authors: de Langen Pierre , Ballester Benoit 
Published: May 2024

Abstract
The large diversity of functional genomic assays allows for the characterization of non-coding and coding events at the tissue level or at a single-cell resolution. However, this diversity also leads to protocol differences, widely varying sequencing depths, substantial disparities in sample sizes, and number of features. In this work, we have built a Python package, MUFFIN, which offers a wide variety of tools suitable for a broad range of genomic assays and brings many tools that were missing from the Python ecosystem. First, MUFFIN has specialized tools for the exploration of the non-coding regions of genomes, such as a function to identify consensus peaks in peak-called assays, as well as linking genomic regions to genes and performing Gene Set Enrichment Analyses. MUFFIN also possesses a robust and flexible count table processing pipeline, comprising normalization, count transformation, dimensionality reduction, Differential Expression, and clustering. Our tools were tested on three widely different scRNA-seq, ChIP-seq and ATAC-seq datasets. MUFFIN integrates with the popular Scanpy ecosystem and is available on Conda and at https://github.com/pdelangen/Muffin.
Clinical experiences and learning curves from robot-assisted neurosurgical biopsies with Stealth Autoguide™
Authors: Ljungqvist Johan , Barchéus Hanna , Abbas Fatima , Ozanne Anneli , Nilsson Daniel , Corell Alba 
Published: May 2024

Abstract

Background
Biopsies of intracranial lesions are a cornerstone in the diagnosis of unresectable tumors to guide neurooncological treatment; however, the procedure is also associated with risks. The results from the cranial robot guidance system Stealth Autoguide™ were studied after introduction at a neurosurgical department. Primary aims include the presentation of clinical and radiological data, accuracy of radiological diagnosis, learning curves of the new technology, diagnostic yield, and precision. The secondary aim was to study complications.

Methods
Retrospective data inclusion was performed on patients ≥ 18 years undergoing biopsy with Stealth Autoguide™ due to suspected brain tumors in the first 3 years after the introduction of the technique. Data regarding clinical characteristics, intraoperative variables, pathological diagnosis, and complications were recorded. Analyses of learning curves were performed.

Results
A total of 79 procedures were performed on 78 patients with a mean age of 62 years (SD 12.7, range 23–82), 30.8% were female. Tumors were often multifocal (63.3%) and supratentorial (89.9%). The diagnostic yield was 87.3%. The first-hand radiological diagnosis was correct in 62.0%. A slight decrease in operation time was observed, although not significant. The surgeon contributed to 12% of the variability.

Conclusions
Robot-assisted biopsies with Stealth Autoguide™ seem to be comparable, with regards to complications, to frame-based and other frameless neurosurgical biopsies. Learning curves demonstrated no statistical differences in time of surgery and only 12% surgeon-related variation (ie, variation caused by the change of performing surgeon), suggesting a successful implementation of this technical adjunct.
Unmet Needs for Ancillary Services by Provider Type Among People With Diagnosed Human Immunodeficiency Virus
Authors: Thomas Celina , Yuan Xin , Taussig Jennifer A , Tie Yunfeng , Dasgupta Sharoda , Riedel David J , Weiser John 
Published: May 2024

Abstract

Background
Unmet needs for ancillary services are substantial among people with human immunodeficiency virus (PWH), and provider type could influence the prevalence of unmet needs for these services.

Methods
Data from a national probability sample of PWH were analyzed from the Centers for Disease Control and Prevention’s Medical Monitoring Project. We analyzed 2019 data on people who had ≥1 encounter with a human immunodeficiency virus (HIV) care provider (N = 3413) and their care facilities. We assessed the proportion of needs that were unmet for individual ancillary services, overall and by HIV care provider type, including infectious disease (ID) physicians, non-ID physicians, nurse practitioners, and physician assistants. We calculated prevalence differences (PDs) with predicted marginal means to assess differences between groups.

Results
An estimated 98.2% of patients reported ≥1 need for an ancillary service, and of those 46% had ≥1 unmet need. Compared with patients of ID physicians, needs for many ancillary services were higher among patients of other provider types. However, even after adjustment, patients of non-ID physicians had lower unmet needs for dental care (adjusted PD, −5.6 [95% confidence interval {CI}, −9.9 to −1.3]), and patients of nurse practitioners had lower unmet needs for HIV case management services (adjusted PD, −5.4 [95% CI, −9.4 to −1.4]), compared with patients of ID physicians.

Conclusions
Although needs were greater among patients of providers other than ID physicians, many of these needs may be met by existing support systems at HIV care facilities. However, additional resources may be needed to address unmet needs for dental care and HIV case management among patients of ID physicians.
Genotyping-by-sequencing-based high-resolution mapping reveals a single candidate gene for the grapevine veraison locus Ver1
Authors: Frenzke Lena , Röckel Franco , Wenke Torsten , Schwander Florian , Grützmann Konrad , Naumann Julia , Zakrzewski Falk , Heinekamp Tom , Maglione Maria , Wenke Anja , Kögler Anja , Zyprian Eva , Dahl Andreas , Förster Franz , Töpfer Reinhard , Wanke Stefan 
Published: May 2024

Abstract
Veraison marks the transition from berry growth to berry ripening and is a crucial phenological stage in grapevine (Vitis vinifera): the berries become soft and begin to accumulate sugars, aromatic substances, and, in red cultivars, anthocyanins for pigmentation, while the organic acid levels begin to decrease. These changes determine the potential quality of wine. However, rising global temperatures lead to earlier flowering and ripening, which strongly influence wine quality. Here, we combined genotyping-by-sequencing with a bioinformatics pipeline on ∼150 F1 genotypes derived from a cross between the early ripening variety “Calardis Musqué” and the late-ripening variety “Villard Blanc”. Starting from 20,410 haplotype-based markers, we generated a high-density genetic map and performed a quantitative trait locus analysis based on phenotypic datasets evaluated over 20 yrs. Through locus-specific marker enrichment and recombinant screening of ∼1,000 additional genotypes, we refined the originally postulated 5-mb veraison locus, Ver1, on chromosome 16 to only 112 kb, allowing us to pinpoint the ethylene response factor VviERF027 (VCost.v3 gene ID: Vitvi16g00942, CRIBIv1 gene ID: VIT_16s0100g00400) as veraison candidate gene. Furthermore, the early veraison allele could be traced back to a clonal “Pinot” variant first mentioned in the seventeenth century. “Pinot Precoce Noir” passed this allele over “Madeleine Royale” to the maternal grandparent “Bacchus Weiss” and, ultimately, to the maternal parent “Calardis Musqué”. Our findings are crucial for ripening time control, thereby improving wine quality, and for breeding grapevines adjusted to climate change scenarios that have a major impact on agro-ecosystems in altering crop plant phenology.
Incorporating platinum circular economy into China’s hydrogen pathways toward carbon neutrality
Authors: Wang Peng , Wang Chenyang , Li Jiashuo , Hubacek Klaus , Sun Laixiang , Yang Fan , Feng Kuishuang , Chen Wei-Qiang 
Published: May 2024

Abstract
Hydrogen is gaining tremendous traction in China as the fuel of the future to support the country’s carbon neutrality ambition. Despite that hydrogen as fuel largely hinges on the supply of platinum (Pt), the dynamic interlinkage between Pt supply challenges, hydrogen development pathways, and climate targets in China has yet to be deeply analyzed. Here, we adopt an integrated assessment model to address this important concern and corresponding strategies for China. The results indicate that the booming hydrogen development would drive China’s cumulative demand for Pt metal to reach 4,200–5,000 tons. Much of this demand, met through a limited supply pattern, is vulnerable to price volatility and heightened geopolitical risks, which can be mitigated through circular economy strategies. Consequently, a coordinated approach to leverage both global sustainable Pt sourcing and a robust domestic Pt circular economy is imperative for ensuring cost-effective hydrogen production, aligned with a climate-safe future.
Unsettled belief
Authors: Beddor Bob 
Published: May 2024

Abstract
According to many philosophers, belief is a settling state. On this view, someone who believes p is disposed to take p for granted in practical and theoretical reasoning. This paper presents a simple objection to this settling conception of belief: it conflicts with our ordinary patterns of belief ascription. I show that ascriptions of unsettled beliefs are commonplace, and that they pose problems for all of the most promising ways of developing the settling conception. I proceed to explore the implications of my argument for the relation between belief and credence, and for the relative importance of belief in psychological explanation.
Smokers’ perception of the comparative health risks of cigarettes, e-cigarettes and heated tobacco products: a survey among the German population
Authors: Klosterhalfen Stephanie , Kotz Daniel , Kastaun Sabrina 
Published: May 2024

Abstract

Background
Tobacco cigarettes, e-cigarettes and heated tobacco products can pose different health risks (harm continuum). As current tobacco smokers could benefit from switching to less harmful products, we aimed to assess current smokers’ perceived comparative health risks of these three products and to explore associations between risk perceptions and specific user characteristics.

Methods
We analysed data from 11 waves (2019–2021; N = 5657 current tobacco smokers) of a representative, cross-sectional household survey conducted in Germany. Associations were assessed with multivariable logistic regression models.

Results
55.2% of smokers (95%CI = 53.8–56.5%) ranked cigarettes as the most harmful product. 36.1% of smokers (95%CI = 34.8–37.3%) perceived e-cigarettes and 33.8% (95%CI = 32.5–35.0%) heated tobacco products as more harmful than cigarettes. Misperceptions that e-cigarettes or heated tobacco products are more harmful to health than cigarettes increased over the 3-year study period and were more common among those with lower educational attainment.

Conclusions
Only half of current tobacco smokers in Germany perceive the comparative health risks of cigarettes adequately and such misperceptions have increased recently. As current smokers could benefit most from switching to less harmful products, educational campaigns are needed to inform this group about the health risks of tobacco smoking and the comparative health risks of the various nicotine and tobacco products along the harm continuum.
The bird tear-drinking moths of the genus Hemiceratoides (Lepidoptera: Erebidae)
Authors: Zilli Alberto , Barbut Jérôme , Dorward Leejiah J , Lees David C 
Published: May 2024

Abstract
New footage confirms Hemiceratoides moths to be bird tear-drinking. Bionomics of Hemiceratoides is updated, and its taxonomy revised, with descriptions of Hemiceratoides ornithopotissp. nov. and H. avimolestumsp. nov., while Cynisca thysbe, type species of Siccyna (= Cynisca), is recombined as H. thysbecomb. nov. (thus Hemiceratoides = Siccynasynon. nov.), whereas another Siccyna, originally Cynisca reichi, is found to be conspecific with Devena atomifera(synon. nov.). We highlight the striking proboscis modifications in Hemiceratoides compared to non-calpine erebids that may perhaps be incidental eye frequenters. Hemiceratoides sittaca has remarkable, sexually dimorphic labial palps, which are fang-like in males, probably assisting in tear feeding. Hemiceratoides also features unusual valval processes, an asymmetric whip- or stick-like juxta, and sclerotizations surrounding the ostium bursae. A phylogenetic tree reconstructed with eight nuclear genes as well as COI for the subfamilies Hypocalinae + Calpinae confirms the prior finding that Hemiceratoides belongs to tribe Ophiderini, not to Calpini, and supports previously held relationships between calpine genera, except that (Miniodes + Phyllodes) do not form a sister group relationship with (Hemiceratoides + Eudocima). We thus discuss the controversy over the evolution of the unusual feeding habits in Hemiceratoides. Finally, Calyptra canadensiscomb. rev. is updated due to a newly established synonymy Calyptra = Percalpesynon. nov.
Hereditary angioedema: current therapeutic management and future approaches
Authors: Lamacchia Donatella , Nappi Emanuele , Marzio Valentina , Locatelli Francesca , Messina Maria Rita , Heffler Enrico 
Published: May 2024

Purpose of review
The aim of this review is to provide an account of the focus of therapeutic strategies for hereditary angioedema (HAE), give a brief overview of those used in the past and set aside and toughly discuss those currently available as first line. Further research is ongoing and the future therapeutic approaches that are still in different phases of study will be reviewed as well.

Recent findings
In the last two decades, major research advancements on HAE pathophysiology and management were made and numerous novel therapeutic options are now available. Compared to the past, drugs available nowadays are more effective, well tolerated, and possibly have a more convenient administration route. Moreover, numerous other drugs with innovative mechanisms of action are under development.

Summary
HAE is a rare genetic disease that if not promptly treated, it can lead to death from asphyxiation. Furthermore, due to its disfiguring and painful manifestations, HAE implies an important burden on the quality of life. Recently, following great research progresses on HAE therapy, evidence-based guidelines on HAE management were released. The therapeutic landscape of HAE is still under florid development, and it is possible novel treatments will remarkably revolutionize HAE management in the future.
Application of machine learning in the analysis of multiparametric MRI data for the differentiation of treatment responses in breast cancer: retrospective study
Authors: Wang Jinhua , Wang Liang , Yang Zhongxian , Tan Wanchang , Liu Yubao 
Published: May 2024

Objective
The objective of this study is to develop and validate a multiparametric MRI model employing machine learning to predict the effectiveness of treatment and the stage of breast cancer.

Methods
The study encompassed 400 female patients diagnosed with breast cancer, with 200 individuals allocated to both the control and experimental groups, undergoing examinations in Shenzhen, China, during the period 2017–2023. This study pertains to retrospective research. Multiparametric MRI was employed to extract data concerning tumor size, blood flow, and metabolism.

Results
The model achieved high accuracy, predicting treatment outcomes with an accuracy of 92%, sensitivity of 88%, and specificity of 95%. The model effectively classified breast cancer stages: stage I, 38% (P = 0.027); stage II, 72% (P = 0.014); stage III, 50% (P = 0.032); and stage IV, 45% (P = 0.041).

Conclusions
The developed model, utilizing multiparametric MRI and machine learning, exhibits high accuracy in predicting the effectiveness of treatment and breast cancer staging. These findings affirm the model’s potential to enhance treatment strategies and personalize approaches for patients diagnosed with breast cancer. Our study presents an innovative approach to the diagnosis and treatment of breast cancer, integrating MRI data with machine learning algorithms. We demonstrate that the developed model exhibits high accuracy in predicting treatment efficacy and differentiating cancer stages. This underscores the importance of utilizing MRI and machine learning algorithms to enhance the diagnosis and individualization of treatment for this disease.