bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local adaptation, recombination, and the fate of neopolyploids
Authors: McDaniel Stuart F. 
Published: July 2024

SummaryPolyploidy is widely recognized as an important speciation mechanism because it isolates tetraploids from their diploid progenitors. Polyploidy also provides new genetic material that may facilitate adaptive evolution. However, new mutations are more likely to arise after a neopolyploid has already successfully invaded a population. Thus, the role of adaptive forces in establishing a polyploid remains unclear. One solution to this apparent paradox may lie in the capacity of polyploids to suppress recombination among preexisting locally adapted alleles. The local adaptation mechanism requires that spatially heterogeneous selection acts on multiple loci and that gene flow introduces maladapted alleles to the population where the polyploid forms. The mechanism requires neither strong genetic drift nor any intrinsic benefit of genome doubling and can accommodate any mode of gene action. A unique prediction of the mechanism is that adaptive alleles should predate polyploidization, a pattern consistent with observations from a few well‐studied polyploids. The mechanism is also consistent with the coexistence of both diploid and tetraploid cytotypes, fitness heterogeneity among independently derived polyploids, and the prevalence of outcrossing among older polyploids. The local adaptation mechanism also makes novel predictions about circumstances favoring polyploid invasions that can be tested using molecular genetic or comparative approaches.
Efficacy and safety of sublingual immunotherapy using house dust mite tablet for 1–4 years old children with perennial allergic rhinitis
Authors: Sasamoto Koki , Nagakura Ken‐ichi , Asaumi Tomoyuki , Fusayasu Naoko , Ohashi‐Doi Katsuyo , Yanagida Noriyuki , Sato Sakura , Ebisawa Motohiro 
Published: July 2024

AbstractBackgroundSublingual immunotherapy (SLIT) for perennial allergic rhinitis (AR) has not been extensively studied in preschoolers. We investigated the efficacy and safety of house dust mite (HDM) SLIT‐tablet for children aged 1–4 years.MethodsChildren aged 1–4 years with AR were divided into SLIT (n = 22) and control (n = 12) groups based on their guardians' preferences. The SLIT group received a daily dose of 10,000 JAU of HDM SLIT‐tablet for 12 months, whereas the control group received symptomatic treatment only.ResultsThe baseline median age was 41 and 34 months in the SLIT and control groups, respectively, and the median AR symptom score was 4 for both groups. Compared with baseline, the AR symptom score had decreased significantly in the SLIT group after 12 months (score: 3, p = .002), whereas it tended to increase in the control group (score: 6, p = .08). Adverse reactions to SLIT were mild and occurred in eight patients (36%). In the SLIT group, Dermatophagoides (D.) farinae‐specific IgE (sIgE) levels increased during the first 6 months and decreased to baseline levels at 12 months. In the control group, D. farinae‐sIgE levels had increased significantly at 12 months compared to baseline (p = .01). D. farinae‐specific IgG4 and HDM IgE‐blocking factor levels were significantly increased at 12 months compared to baseline in the SLIT group only (p < .001). A lower wheezing frequency was seen in the SLIT group (0.3%) compared to the control group (0.7%).ConclusionThis pilot study demonstrated the efficacy, safety, and immunomodulatory effects of HDM SLIT‐tablet in preschoolers with AR.
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Unravelling the genetic basis and regulation networks related to fibre quality improvement using chromosome segment substitution lines in cotton
Authors: Qi Guoan , Si Zhanfeng , Xuan Lisha , Han Zegang , Hu Yan , Fang Lei , Dai Fan , Zhang Tianzhen 
Published: July 2024

SummaryThe elucidation of genetic architecture and molecular regulatory networks underlying complex traits remains a significant challenge in life science, largely due to the substantial background effects that arise from epistasis and gene–environment interactions. The chromosome segment substitution line (CSSL) is an ideal material for genetic and molecular dissection of complex traits due to its near‐isogenic properties; yet a comprehensive analysis, from the basic identification of substitution segments to advanced regulatory network, is still insufficient. Here, we developed two cotton CSSL populations on the Gossypium hirsutum background, representing wide adaptation and high lint yield, with introgression from G. barbadense, representing superior fibre quality. We sequenced 99 CSSLs that demonstrated significant differences from G. hirsutum in fibre, and characterized 836 dynamic fibre transcriptomes in three crucial developmental stages. We developed a workflow for precise resolution of chromosomal substitution segments; the genome sequencing revealed substitutions collectively representing 87.25% of the G. barbadense genome. Together, the genomic and transcriptomic survey identified 18 novel fibre‐quality‐related quantitative trait loci with high genetic contributions and the comprehensive landscape of fibre development regulation. Furthermore, analysis determined unique cis‐expression patterns in CSSLs to be the driving force for fibre quality alteration; building upon this, the co‐expression regulatory network revealed biological relationships among the noted pathways and accurately described the molecular interactions of GhHOX3, GhRDL1 and GhEXPA1 during fibre elongation, along with reliable predictions for their interactions with GhTBA8A5. Our study will enhance more strategic employment of CSSL in crop molecular biology and breeding programmes.
Cutaneous legionellosis in an immunocompromised neonate
Authors: Alzahrani Nujood , Monir Reesa L. , Patel Pratik A. , Fox Thomas G. , Gonzalez Mark D. , Lawley Leslie 
Published: July 2024

AbstractCutaneous Legionella infection is rare and primarily seen in immunosuppressed patients. Herein, we present a case of cutaneous and pulmonary legionellosis presenting with fever and erythematous subcutaneous nodules in a neonate with severe combined immunodeficiency. This case underscores the importance of considering this diagnosis and highlights the use of modern testing modalities to promptly diagnose and treat infections in immunocompromised patients.
A New Opening for the Alternative Punishments Debate: Applying the Extended Mind Thesis
Authors: Mamak Kamil 
Published: July 2024

AbstractThe debate on alternative punishments appears to be stagnating. The impasse may be overcome if we consider humans from a different philosophical perspective. If we answer differently the question of who we are punishing, we open new possibilities regarding the question of how we punish. In particular, by applying the extended mind thesis we can arrive at interesting outcomes and reopen the debate on alternative punishments. According to this theory, external artifacts—such as smartphones—can be considered part of our minds. In this article, I defend the thesis that restricting access to personal technologies that are a part of one's self should be considered a form of punishment. Thus, a human who is considered from an extended perspective can be punished in a new way.
Classification of spatial dynamics of a vector–host epidemic model in advective heterogeneous environment
Authors: Feng Yuwei , Wang Jinliang 
Published: July 2024

AbstractIn this paper, we propose and analyze a reaction–diffusion vector–host disease model with advection effect in an one‐dimensional domain. We introduce the basic reproduction number (BRN) and establish the threshold dynamics of the model in terms of . When there are no advection terms, we revisit the asymptotic behavior of w.r.t. diffusion rate and the monotonicity of under certain conditions. Furthermore, we obtain the asymptotic behavior of under the influence of advection effects. Our results indicate that when the advection rate is large enough relative to the diffusion rate, tends to be the value of local basic reproduction number (LBRN) at the downstream end, which enriches the asymptotic behavior results of the BRN in nonadvection heterogeneous environments. In addition, we explore the level set classification of , that is, there exists a unique critical surface indicating that the disease‐free equilibrium is globally asymptotically stable on one side of the surface, while it is unstable on the other side. Our results also reveal that the aggregation phenomenon will occur, namely, when the ratio of advection rate to diffusion rate is large enough, infected individuals will gather at the downstream end.
The coupled Hirota equations with a 3×3$3\times 3$ Lax pair: Painlevé‐type asymptotics in transition zone
Authors: Zhao Xiaodan , Wang Lei 
Published: July 2024

AbstractWe consider the Painlevé asymptotics for a solution of the integrable coupled Hirota equations with a Lax pair whose initial data decay rapidly at infinity. Using the Riemann–Hilbert (RH) techniques and Deift–Zhou nonlinear steepest descent arguments, in a transition zone defined by , where is a constant, it turns out that the leading‐order term to the solution can be expressed in terms of the solution of a coupled Painlevé II equations, which are associated with a matrix RH problem and appear in a variety of random matrix models.
Online information about oral health in autism spectrum disorder: Is it good enough?
Authors: Flaifl Yara , Hassona Yazan , Altoum Dana , Flaifl Nada , Taimeh Dina 
Published: July 2024

AbstractIntroductionThe use of the internet has surged significantly over the years. Patients and caregivers of patients with autism spectrum disorder (ASD) might consult the internet for oral health‐related information. Hence, this study aimed to assess the quality and readability of online information available in the English language regarding oral health in ASD.MethodsOnline search using Google.com was conducted using the terms “Autism and dental care,” “Autism and oral health,” and “Autism and dentistry”. The first 100 websites for each term were screened. Quality of information was assessed using the Patient Education Materials Assessment Tool for printed material (PEMAT‐P) and the Journal of American Medical Association (JAMA) benchmarks. A PEMAT score higher than 70% is considered acceptable for readability and actionability. The JAMA benchmarks are authorship, attribution, disclosure, and currency. Readability was evaluated using the Flesch reading ease score and Simple Measure of Gobbledygook (SMOG) readability formula.ResultsOut of the 300 screened websites, 66 were eventually included. The mean PEMAT understandability and actionability scores were 77.13%, and 42.12%, respectively. Only 12.1% of the websites displayed all four JAMA benchmarks. The mean Flesch score was 10th–12th grade level, and the mean SMOG score was 10th grade level.ConclusionWhile the understandability of the information was acceptable, the readability and actionability were too challenging for lay people. Health care professionals and organizations involved in patient education should place more efforts in promoting the quality of online information targeting patients with ASD.
THEORETICAL A‐GRAMMATISM: THE CASE FOR AN ELIMINATIVIST MINIMALISM
Authors: Pañeda Claudia , Lorenzo Guillermo 
Published: July 2024

AbstractThis paper explores patterns of cross‐linguistic, intra‐linguistic and individual variation in the acceptability of sentences with extraction from islands, a classic object of attention of generative grammar. It asks which “competence” concept better fits the presented data. We contrast two alternative views: one that ascribes a multilingual competence to individual speakers, in the “rich competence” tradition of acquisition theory, and another one based on a “competence‐free” kind of model, which is framed as an instantiation of the minimalist approach to the language faculty. We conclude that the latter eliminativist approach is better suited to account for variation in the acceptability of island sentences.
Effects of composite soil conditioner on soil properties and corn yield in a saline–alkali soil
Authors: Fang Yuhang , Huang Hongyan , Wang Xueping , Zhao Yuan , Gao Yan , Cui Xuejun 
Published: July 2024

AbstractBiochar is widely used in agricultural production because of its ability to improve the physical and chemical properties of soil and promote crop growth. In this study, a combination of different biochar and lake sediments were used to improve saline soils. The four raw materials, including corn stalk and chicken manure liquefaction product (SMLP), rice husk charcoal (RHC) and two types of sediment (S‐1 and S‐2), which was used to improve the saline–alkali soil, respectively. The most significantly effective applied on the soil was when the composite soil conditioner (CSC) prepared by mixing SMLP, RHC, S‐1 and S‐2 at 5:20:6000:500 t·100 ha−1. The results of soil experiments using the above blending levels showed that the spike weight, plant height and root length of corn increased by 12.49%, 47.17% and 22.10%, respectively, and the pH and electrical conductivity (EC) of soil decreased by 4.83% and 24.02%, respectively. The contents of soil nutrients, soil organic matter (SOM), water content (WC) and soluble cations (K+, Ca2+ and Mg2+) all presented an increasing trend, and the contents of Na+ and soluble anions (Cl−, CO32−, HCO3− and SO42−) of soil showed a downward trend. Accordingly, the composite soil conditioner with biochar and dredged sediment achieves a synergistic improvement in soil physical structure and an increase in nutrient content, which is beneficial for promoting the growth characteristics and yield of corn.
Introducing the Task as a Challenge Does Not Mitigate the Negative Effect of Gender Stereotype Threat on Motor Skill Learning in Adolescents
Authors: Soltanifar Sara , Abedanzadeh Rasool , Ahmadinezhad Adele , Mousavi Seyyed Mohammadreza 
Published: July 2024

Gender stereotype threat is a sociocultural variable that has received significant attention over the past two decades. We explored whether presenting a task as a practical and challenging activity would reduce the negative impact of implicit activation of gender stereotype threat on motor learning in adolescent girls. Forty-five adolescent girls (Mage ± SD: 13.24 ± 1.06) participated in the study and were asked to throw a tennis ball toward a circular target using their nondominant hand. They were asked to perform five throws as an initial assessment and then were randomly assigned to three groups: IS/CH (i.e., implicit stereotype threat activation and framing the task as a challenge), IS/TH (i.e., implicit stereotype threat activation and framing the task as a threat), and the control (with no instructions). In the IS/CH and IS/TH groups, the participants performed the acquisition phase (five blocks of 10 trials) in the presence of a male evaluator. We used verbal instructions to frame the task as a practical and challenging activity (i.e., learning this task might be a big help in physical education classes in school because it improves throwing skills, and it will help improve control over the nondominant arm which is important in daily activities) and/or threat (i.e., show how good you are on this type of task, and based on your scores, we will be able to measure your natural ability at throwing tasks) before the acquisition phase. One day after the acquisition phase, participants were asked to participate in the retention (10 throws) and transfer tests (10 throws from a distance of 6.5 m). Our findings demonstrated that participants in the control group were able to achieve more effective learning compared with participants in the IS/TH and IS/CH groups. Possible reasons for these results were discussed.
Senataxin mediates R-loop resolution on HPV episomes
Authors: Jose Leny , Smith Keely , Crowner Anaiya , Androphy Elliot J. , DeSmet Marsha 
Published: July 2024

ABSTRACT

Three-stranded DNA–RNA structures known as R-loops that form during papillomavirus transcription can cause transcription–replication conflicts and lead to DNA damage. We found that R-loops accumulated at the viral early promoter in human papillomavirus (HPV) episomal cells but were greatly reduced in cells with integrated HPV genomes. RNA–DNA helicases unwind R-loops and allow for transcription and replication to proceed. Depletion of the RNA–DNA helicase senataxin (SETX) using siRNAs increased the presence of R-loops at the viral early promoter in HPV-31 (CIN612) and HPV-16 (W12) episomal HPV cell lines. Depletion of SETX reduced viral transcripts in episomal HPV cell lines. The viral E2 protein, which binds with high affinity to specific palindromes near the promoter and origin, complexes with SETX, and both SETX and E2 are present at the viral p97 promoter in CIN612 and W12 cells. SETX overexpression increased E2 transcription activity on the p97 promoter. SETX depletion also significantly increased integration of viral genomes in CIN612 cells. Our results demonstrate that SETX resolves viral R-loops to proceed with HPV transcription and prevent genome integration.

IMPORTANCE
Papillomaviruses contain small circular genomes of approximately 8 kilobase pairs and undergo unidirectional transcription from the sense strand of the viral genome. Co-transcriptional R-loops were recently reported to be present at high levels in cells that maintain episomal HPV and were also detected at the early viral promoter. R-loops can inhibit transcription and DNA replication. The process that removes R-loops from the PV genome and the requisite enzymes are unknown. We propose a model in which the host RNA–DNA helicase senataxin assembles on the HPV genome to resolve R-loops in order to maintain the episomal status of the viral genome.
Safety and adherence to medications and self-care advice in oncology (SAMSON): pilot randomised controlled trial protocol
Authors: Dang Thu Ha , Wickramasinghe Nilmini , Jayaraman Prem Prakash , Burbury Kate , Alexander Marliese , Whitechurch Ashley , Quinn Steve , Rowan Gail , Brooks Sally L , Schofield Penelope 
Published: July 2024

IntroductionWith the increasing use of oral anti-cancer medicines (OAMs), research demonstrating the magnitude of the medication non-adherence problem and its consequences on treatments’ efficacy and toxicity is drawing more attention. Mobile phone interventions may be a practical solution to support patients taking OAMs at home, yet evidence to inform the efficacy of these interventions is lacking. The safety and adherence to medications and self-care advice in oncology (SAMSON) pilot randomised control trial (RCT) aims to evaluate the acceptability, feasibility and potential efficacy of a novel digital solution to improve medication adherence (MA) among people with cancer.Methods and analysisThis is a two-arm, 12-week, pilot RCT aiming to enrol 50 adults with haematological, lung or melanoma cancers at an Australian metropolitan specialised oncology hospital, who are taking oral anti-cancer medicines. Participants will be randomised (1:1 allocation ratio) to either the intervention group (SAMSON solution) or the control group (usual care). The primary outcomes are the acceptability and feasibility of SAMSON. The secondary outcomes are MA, toxicity self-management, anxiety and depressive symptoms, health-related quality of life, and parameters relating to optimal intervention strategy. Quantitative data will be analysed on a modified intention-to-treat basis.SummaryWhile multicomponent interventions are increasingly introduced, SAMSON incorporates novel approaches to the solution. SAMSON provides a comprehensive, patient-centred, digital MA intervention solution with seamless integration of a mobile platform with clinical consultations that are evidence-based, theory-based, co-designed and rigorously tested. The pilot trial will determine whether this type of intervention is feasible and acceptable in oncology and will provide a foundation for a future full-scale RCT.Ethics and disseminationPrimary ethics approvals were received from Peter MacCallum Cancer Centre and Swinburne University of Technology Human Research Ethics Committees (HREC/95332/PMCC and 20237273–15836). Results will be disseminated via peer-reviewed publications and presentations at international and national conferences.Trial registration numberThe protocol has been prospectively registered on the Australian New Zealand Clinical Trials Registry with trial registration number (ACTRN12623000472673).
Sodium valproate is associated with cortical thinning of disease-specific areas in juvenile myoclonic epilepsy
Authors: Crespo Pimentel Bernardo , Kuchukhidze Giorgi , Xiao Fenglai , Caciagli Lorenzo , Höfler Julia , Rainer Lucas , Kronbichler Martin , Vollmar Christian , Duncan John S , Trinka Eugen , Koepp Matthias , Wandschneider Britta 
Published: July 2024

BackgroundJuvenile myoclonic epilepsy (JME) is associated with cortical thinning of the motor areas. The relative contribution of antiseizure medication to cortical thickness is unknown. We aimed to investigate how valproate influences the cortical morphology of JME.MethodsIn this cross-sectional study, individuals with JME with and without valproate, with temporal lobe epilepsy (TLE) with valproate and controls were selected through propensity score matching. Participants underwent T1-weighted brain imaging and vertex-wise calculation of cortical thickness.ResultsWe matched 36 individuals with JME on valproate with 36 individuals with JME without valproate, 36 controls and 19 individuals with TLE on valproate. JME on valproate showed thinning of the precentral gyri (left and right, p<0.001) compared with controls and thinning of the left precentral gyrus when compared with JME not on valproate (p<0.01) or to TLE on valproate (p<0.001). Valproate dose correlated negatively with the thickness of the precentral gyri, postcentral gyri and superior frontal gyrus in JME (left and right p<0.0001), but not in TLE.ConclusionsValproate was associated with JME-specific and dose-dependent thinning of the cortical motor regions. This suggests that valproate is a key modulator of cortical morphology in JME, an effect that may underlie its high efficacy in this syndrome.
FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei 
Published: July 2024

Abstract
The Hippo–YAP1 pathway is an evolutionally conserved signaling cascade that controls organ size and tissue regeneration. Dysregulation of Hippo–YAP1 signaling promotes initiation and progression of several types of cancer, including gastric cancer. As the Hippo–YAP1 pathway regulates expression of thousands of genes, it is important to establish which target genes contribute to the oncogenic program driven by YAP1 to identify strategies to circumvent it. In this study, we identified a vital role of forkhead box protein 4 (FOXP4) in YAP1-driven gastric carcinogenesis by maintaining stemness and promoting peritoneal metastasis. Loss of FOXP4 impaired gastric cancer spheroid formation and reduced stemness marker expression, whereas FOXP4 upregulation potentiated cancer cell stemness. RNA sequencing analysis revealed SOX12 as a downstream target of FOXP4, and functional studies established that SOX12 supports stemness in YAP1-induced carcinogenesis. A small-molecule screen identified 42-(2-tetrazolyl) rapamycin as a FOXP4 inhibitor, and targeting FOXP4 suppressed gastric cancer tumor growth and enhanced the efficacy of 5-fluorouracil chemotherapy in vivo. Collectively, these findings revealed that FOXP4 upregulation by YAP1 in gastric cancer regulates stemness and tumorigenesis by upregulating SOX12. Targeting the YAP1–FOXP4–SOX12 axis represents a potential therapeutic strategy for gastric cancer.
Significance: Hippo–YAP1 signaling maintains stemness in gastric cancer by upregulating FOXP4, identifying FOXP4 as a stemness biomarker and therapeutic target that could help improve patient outcomes.