bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation of Ramsey’s theorem for pairs and well-foundedness
Authors: Le Houérou Quentin , Patey Ludovic Levy , Yokoyama Keita 
Published: October 2024

In this article, we prove that Ramsey’s theorem for pairs and two colors is

Π
1
1

\Pi ^1_1

-conservative over

R
C
A

0

+

B

Σ
2
0

+

W
F

(

ϵ
0

)

\mathsf {RCA}_0 + \mathsf {B}\Sigma ^0_2 + \mathsf {WF}(\epsilon _0)

and over

R
C
A

0

+

B

Σ
2
0

+

⋃
n

W
F

(

ω
n
ω

)

\mathsf {RCA}_0 + \mathsf {B}\Sigma ^0_2 + \bigcup _n \mathsf {WF}(\omega ^\omega _n)

. These results improve theorems from Chong, Slaman and Yang [Adv. Math. 308 (2017), pp. 121–141] and Kołodziejczyk and Yokoyama [In search of the first-order part of Ramsey’s theorem for pairs, Springer, Cham, 2021] and belong to a long line of research towards the characterization of the first-order part of Ramsey’s theorem for pairs.
Rapid evasive behaviors of diamondback moth larvae against ants
Authors: Ito Kazuya , Yano Shuichi 
Published: October 2024

Abstract
Larvae of the diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae) wriggle vigorously backward when physically stimulated. To explore whether this behavior is effective against ant attacks on their host plants with three-dimensional structures, we experimentally observed DBM larval movements and consequences thereof when attacked by Formica japonica (Hymenoptera: Formicidae) ants on the upper and lower surfaces of host plant leaves. On the upper surfaces of leaves, DBM larvae wriggled backward in response to ant attacks, and most larvae hung from leaf edges by spinning silk threads. On the lower surfaces of leaves, DBM larvae did not wriggle backward but immediately hung from the lower surface in response to attacks. No ants were able to pursue hanging larvae. We conclude that wriggling backward by DBM larvae belongs to a sequence of evasive movements against ant attacks on upper leaf surfaces. To our knowledge, this is the first report of combined wriggling and hanging behaviors by Lepidopteran larvae that are effective against ants in three-dimensional habitats.
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping
Authors: Li Zuqi , Katz Sonja , Saccenti Edoardo , Fardo David W , Claes Peter , Martins dos Santos Vitor A P , Van Steen Kristel , Roshchupkin Gennady V 
Published: October 2024

Abstract
Unsupervised learning, particularly clustering, plays a pivotal role in disease subtyping and patient stratification, especially with the abundance of large-scale multi-omics data. Deep learning models, such as variational autoencoders (VAEs), can enhance clustering algorithms by leveraging inter-individual heterogeneity. However, the impact of confounders—external factors unrelated to the condition, e.g. batch effect or age—on clustering is often overlooked, introducing bias and spurious biological conclusions. In this work, we introduce four novel VAE-based deconfounding frameworks tailored for clustering multi-omics data. These frameworks effectively mitigate confounding effects while preserving genuine biological patterns. The deconfounding strategies employed include (i) removal of latent features correlated with confounders, (ii) a conditional VAE, (iii) adversarial training, and (iv) adding a regularization term to the loss function. Using real-life multi-omics data from The Cancer Genome Atlas, we simulated various confounding effects (linear, nonlinear, categorical, mixed) and assessed model performance across 50 repetitions based on reconstruction error, clustering stability, and deconfounding efficacy. Our results demonstrate that our novel models, particularly the conditional multi-omics VAE (cXVAE), successfully handle simulated confounding effects and recover biologically driven clustering structures. cXVAE accurately identifies patient labels and unveils meaningful pathological associations among cancer types, validating deconfounded representations. Furthermore, our study suggests that some of the proposed strategies, such as adversarial training, prove insufficient in confounder removal. In summary, our study contributes by proposing innovative frameworks for simultaneous multi-omics data integration, dimensionality reduction, and deconfounding in clustering. Benchmarking on open-access data offers guidance to end-users, facilitating meaningful patient stratification for optimized precision medicine.
Cancerous time estimation for interpreting the evolution of lung adenocarcinoma
Authors: Han Yourui , Chen Bolin , Bian Jun , Kang Ruiming , Shang Xuequn 
Published: October 2024

Abstract
The evolution of lung adenocarcinoma is accompanied by a multitude of gene mutations and dysfunctions, rendering its phenotypic state and evolutionary direction highly complex. To interpret the evolution of lung adenocarcinoma, various methods have been developed to elucidate the molecular pathogenesis and functional evolution processes. However, most of these methods are constrained by the absence of cancerous temporal information, and the challenges of heterogeneous characteristics. To handle these problems, in this study, a patient quasi-potential landscape method was proposed to estimate the cancerous time of phenotypic states’ emergence during the evolutionary process. Subsequently, a total of 39 different oncogenetic paths were identified based on cancerous time and mutations, reflecting the molecular pathogenesis of the evolutionary process of lung adenocarcinoma. To interpret the evolution patterns of lung adenocarcinoma, three oncogenetic graphs were obtained as the common evolutionary patterns by merging the oncogenetic paths. Moreover, patients were evenly re-divided into early, middle, and late evolutionary stages according to cancerous time, and a feasible framework was developed to construct the functional evolution network of lung adenocarcinoma. A total of six significant functional evolution processes were identified from the functional evolution network based on the pathway enrichment analysis, which plays critical roles in understanding the development of lung adenocarcinoma.
SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction
Authors: Chen Tianyi , Wei Xindian , Xie Lianxin , Zhang Yunfei , Liu Cheng , Shen Wenjun , Wu Si , Wong Hau-San 
Published: October 2024

Abstract
The spatial reconstruction of single-cell RNA sequencing (scRNA-seq) data into spatial transcriptomics (ST) is a rapidly evolving field that addresses the significant challenge of aligning gene expression profiles to their spatial origins within tissues. This task is complicated by the inherent batch effects and the need for precise gene expression characterization to accurately reflect spatial information. To address these challenges, we developed SELF-Former, a transformer-based framework that utilizes multi-scale structures to learn gene representations, while designing spatial correlation constraints for the reconstruction of corresponding ST data. SELF-Former excels in recovering the spatial information of ST data and effectively mitigates batch effects between scRNA-seq and ST data. A novel aspect of SELF-Former is the introduction of a gene filtration module, which significantly enhances the spatial reconstruction task by selecting genes that are crucial for accurate spatial positioning and reconstruction. The superior performance and effectiveness of SELF-Former’s modules have been validated across four benchmark datasets, establishing it as a robust and effective method for spatial reconstruction tasks. SELF-Former demonstrates its capability to extract meaningful gene expression information from scRNA-seq data and accurately map it to the spatial context of real ST data. Our method represents a significant advancement in the field, offering a reliable approach for spatial reconstruction.
Cuticular morphology of Schinus L. and related genera
Authors: Matel Theodore P , Gandolfo Maria A , Mitchell John D 
Published: October 2024

Abstract
The Anacardiaceae are a characteristic angiosperm family of the Neotropics where they comprise ~32 genera and 200 species (~80 genera and 800 species globally). Among Neotropical Anacardiaceae genera, Schinus has the greatest species richness with 42 species distributed from tropical latitudes of Brazil and Peru south to the temperate steppe, matorral, and Valdivian temperate forest communities of Patagonia. Previous studies have found some anatomical and morphological leaf traits (e.g. simple vs. compound leaf organization) useful in characterizing lineages within Schinus, but also document traits that are homoplastic within the genus (e.g. stomatal distribution) and convergent among Schinus and its close relatives Lithrea and Mauria (e.g. mesophyll arrangement). Here, we present a survey of leaf cuticular traits in 53 species of Schinus and its closest relatives Lithrea, Mauria, and Euroschinus based on characters observed with scanning electron and optical light microscopy. We use ordinated Bray–Curtis distances based on 18 characters and 2D nonmetric multidimensional scaling to show that cuticular morphology resolves the three most diverse genera, Euroschinus, Mauria, and Schinus, but does not resolve intrageneric sections of Schinus. We propose that a distinctive acuminate gland type occurring only within Euroschinus may constitute a potential synapomorphy for this genus. Within Schinus, we find inconsistency in stomatal distribution among specimens of a single species, among species of a single section, and between sections of the genus, and suggest that current evidence is insufficient to implicate either phenotypic plasticity or homoplasy as the causative mechanism of this variation.
Efficacy and safety of combined topical estradiol with minoxidil vs. topical minoxidil in female pattern hair loss: a trichoscopic randomized controlled trial
Authors: Bedair Nermeen Ibrahim , EL-Komy Mohamed H M , Mohamed Rania Elsayed , Shamma Rehab Nabil , Amer Marwa Ahmed 
Published: October 2024

Abstract

Background
Female pattern hair loss (FPHL) is common and has a negative impact on quality of life. FPHL is more challenging to treat than male pattern hair loss, with minoxidil being the gold standard treatment. Several studies have used 17α-estradiol solution for treating FPHL with variable results, either alone or combined with minoxidil.

Objectives
To study the safety and efficacy of topical 17α-ethinylestradiol 0.01% combined with minoxidil 2% in comparison with minoxidil 2% in the treatment of FPHL.

Methods
Forty-three women with FPHL were recruited to this randomized controlled study and were asked to blindly apply twice daily six puffs of a spray-on solution containing either 17α-ethinylestradiol 0.01% combined with minoxidil 2% (EMX group) or minoxidil 2% alone (MX group). Treatment continued for 6 months. Clinical and trichoscopic assessments were performed at baseline and at the end of the treatment.

Results
At the end of the treatment period, both groups showed signs of improvement. Improvement parameters were better for the EMX group vs. the MX group, but this was not statistically significant. More patients in the EMX group experienced menstrual irregularities. Limitations include the limited number of patients and follow-up period. Also, the effects of estradiol were not studied on a cellular or molecular levels and systemic absorption of both medications was not determined.

Conclusions
The use of a 0.01% 17α-ethinylestradiol with a 2% minoxidil solution in the treatment of FPHL does not seem to offer a statistically significant advantage compared with minoxidil alone and may carry a higher risk of associated menstrual irregularities.
Differential water deprivation tolerances of adult Rhagoletis indifferens and Rhagoletis pomonella (Diptera: Tephritidae) as a possible factor affecting their distributional abundances in Washington State, USA
Authors: Yee Wee L , Rose Alexander C , Milnes Joshua M , Feder Jeffrey L 
Published: October 2024

Abstract
Insects that evolved in mesic regions may have difficulty establishing in xeric regions. Rhagoletis pomonella (Walsh) (Diptera: Tephritidae) was introduced into drier western North America from mesic eastern North America while Rhagoletis indifferens Curran is native to western North America. Here, we predicted that R. indifferens survives water deprivation longer than R. pomonella, as R. indifferens is more abundant than R. pomonella in dry central Washington (WA) State, USA. Sweet and bitter cherry-origin R. indifferens and apple- and hawthorn-origin R. pomonella from xeric central or mesic western WA were provided water throughout or were water-deprived at 2–4 and 14–18 d old and held at 20°C or 30/31°C and daily survival recorded. At 20°C and 30°C, western WA apple-origin R. pomonella provided water survived longer than sweet cherry-origin R. indifferens. When water-deprived, however, 2–4 d old R. indifferens, although smaller, survived significantly longer than western WA apple-origin R. pomonella of the same age. This was also generally true for 14–18 d old flies, although differences were less often significant. Central WA large-thorn hawthorn-origin R. pomonella survived water deprivation significantly longer than western WA apple-origin R. pomonella, and as long as R. indifferens. Water-deprived flies of both species survived longer at 20°C than 30/31°C. Survival analyses suggest that low water availability rather than high temperature contributes to lower R. pomonella than R. indifferens abundances in central WA, with R. pomonella populations in that region differing from western WA R. pomonella with respect to tolerance of xeric climates.
Systolic anterior motion-mediated mitral regurgitation and surgical management in hypertrophic obstructive cardiomyopathy
Authors: Wang Hui , Zhu Ying , Quintana Eduard , Ibáñez Cristina , Deng Youbin , Wei Xiang , Liu Yani 
Published: October 2024

Summary
Mitral regurgitation mediated by systolic anterior motion is a typical manifestation in patients with hypertrophic obstructive cardiomyopathy. Although septal myectomy is currently the preferred treatment for patients with drug-refractory hypertrophic obstructive cardiomyopathy, surgical management of associated mitral regurgitation remains controversial. Whether septal myectomy alone or additional valve procedures are required to correct significant mitral regurgitation depends largely on the pathophysiology of each individual. For intervention purposes, it is important to identify the real systolic anterior motion-mediated mitral regurgitation and clarify the mitral structural abnormalities, as well as the other conditions, which may indicate the degree of mitral valve competence. As a first-line imaging modality in the management of hypertrophic cardiomyopathy, echocardiography could provide crucial information for surgical decision making. In this article, we focus on elucidating the typical echocardiographic features of systolic anterior motion-mediated mitral regurgitation and offer an assessment process to determine other contributors to obstruction and mitral regurgitation. Additionally, guidance for surgical decision making for mitral regurgitation in patients with hypertrophic obstructive cardiomyopathy is discussed.
Farmers’ adoption of organic agriculture—a systematic global literature review
Authors: Möhring Niklas , Muller Adrian , Schaub Sergei 
Published: October 2024

Abstract
Policymakers worldwide set ambitious targets to increase the share of organic farming. We conduct a global, systematic literature review to synthesise evidence on the adoption of organic farming and support policymakers and food-value chain actors in reaching policy goals. First, we map the existing research and identify substantial gaps regarding the research focus, methodology and geographical coverage. Second, using a conceptual framework of the farmers’ adoption process, we provide an overview of evidence-based recommendations to scale organic adoption. Finally, using regression analysis, we show that especially the organic market maturity and the level of agricultural productivity matter for the type of recommended measures.
Intra-operative and post-operative management of conduits for coronary artery bypass grafting: a clinical consensus statement of the European Society of Cardiology Working Group on Cardiovascular Surgery and the European Association for Cardio-Thoracic Surgery Coronary Task Force
Authors: Sandner Sigrid , Antoniades Charalambos , Caliskan Etem , Czerny Martin , Dayan Victor , Fremes Stephen E , Glineur David , Lawton Jennifer S , Thielmann Matthias , Gaudino Mario 
Published: October 2024

Abstract
The structural and functional integrity of conduits used for coronary artery bypass grafting is critical for graft patency. Disruption of endothelial integrity and endothelial dysfunction are incurred during conduit harvesting subsequent to mechanical or thermal injury and during conduit storage prior to grafting, leading to acute thrombosis and early graft failure. Late graft failure, in particular that of vein grafts, is precipitated by progressive atherogenesis. Intra-operative management includes appropriate selection of conduit-specific harvesting techniques and storage solutions. Arterial grafts are prone to vasospasm subsequent to surgical manipulation, and application of intra-operative vasodilatory protocols is critical. Post-operative management includes continuation of oral vasodilator therapy and selection of antithrombotic and lipid-lowering agents to attenuate atherosclerotic disease progression in conduits. In this review, the scientific evidence underlying the key aspects of intra- and post-operative management of conduits for coronary artery bypass grafting is examined. Clinical consensus statements for best clinical practice are provided, and areas requiring further research are highlighted.
Durable Immune Response and Long-term Efficacy of COVID-19 Vaccination in Children With Inflammatory Bowel Disease
Authors: Kastl Arthur J , Brenner Erica J , Weaver Kimberly N , Zhang Xian , Strople Jennifer A , Adler Jeremy , Dubinsky Marla C , Bousvaros Athos , Watkins Runa , Dai Xiangfeng , Chen Wenli , Cross Raymond K , Higgins Peter D R , Ungaro Ryan C , Bewtra Meenakshi , Bellaguarda Emanuelle A , Farraye Francis A , Chun Kelly Y , Zikry Michael , Bastidas Monique , Firestine Ann M , Craig Riley G , Boccieri Margie E , Long Millie D , Kappelman Michael D 
Published: October 2024

Abstract

Background
Children with inflammatory bowel disease (IBD) may have diminished serologic response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination and increased risk for subsequent severe coronavirus disease 2019 (COVID-19) infection. We sought to describe outcomes among those who developed SARS-CoV-2 infection following vaccination, characterize SARS-CoV-2 antibodies 1 year post-vaccination, and identify factors associated with durable serologic response.

Methods
We recruited children with IBD who received ≥2 doses of SARS-CoV-2 vaccine and prospectively collected data on (1) demographics, IBD characteristics, and therapy and (2) SARS-CoV-2 vaccination, testing, and infection symptoms. Serum was obtained for measurement of anti-receptor-binding domain IgG antibodies following a 2-part immunization at 12 and 52 weeks.

Results
We enrolled 298 participants (mean age 11.9 ± 3.82, 50% female, 67% Crohn’s disease). Symptomatic COVID-19 infection after vaccination occurred in half of the participants, although only 2 (1%) required hospitalization. Anti-tumor necrosis factor alpha (TNF-α) was associated with higher likelihood of symptomatic COVID-19 infection, with an adjusted hazard ratio of 2.7 (95% CI, 1.5-5.0; P = .001). Nearly all participants (99%) had detectable antibody at Week 52. Children aged 1-5 years had lower 52-week antibody level compared to older children (P = .04), as did those on anti-TNF-α therapy (P = .007) and those who received only 2 vaccine doses prior to Week 52 (P &lt; .001).

Conclusions
SARS-CoV-2 vaccination provides lasting serologic response and protection against severe COVID-19 for most children with IBD, despite the use of lower vaccine doses in younger children and wide-ranging classes of immunosuppressive therapies.
Device-measured stationary behaviour and cardiovascular and orthostatic circulatory disease incidence
Authors: Ahmadi Matthew N , Coenen Pieter , Straker Leon , Stamatakis Emmanuel 
Published: October 2024

Abstract

Background
Previous studies have indicated that standing may be beneficially associated with surrogate metabolic markers, whereas more time spent sitting has an adverse association. Studies assessing the dose-response associations of standing, sitting and composite stationary behaviour time with cardiovascular disease (CVD) and orthostatic circulatory disease are scarce and show an unclear picture.

Objective
To examine associations of daily sitting, standing and stationary time with CVD and orthostatic circulatory disease incidence

Methods
We used accelerometer data from 83 013 adults (mean age ± standard deviation = 61.3 ± 7.8; female = 55.6%) from the UK Biobank to assess daily time spent sitting and standing. Major CVD was defined as coronary heart disease, heart failure and stroke. Orthostatic circulatory disease was defined as orthostatic hypotension, varicose vein, chronic venous insufficiency and venous ulcers. To estimate the dose-response hazard ratios (HR) we used Cox proportional hazards regression models and restricted cubic splines. The Fine–Gray subdistribution method was used to account for competing risks.

Results
During 6.9 (±0.9) years of follow-up, 6829 CVD and 2042 orthostatic circulatory disease events occurred. When stationary time exceeded 12 h/day, orthostatic circulatory disease risk was higher by an average HR (95% confidence interval) of 0.22 (0.16, 0.29) per hour. Every additional hour above 10 h/day of sitting was associated with a 0.26 (0.18, 0.36) higher risk. Standing more than 2 h/day was associated with an 0.11 (0.05, 0.18) higher risk for every additional 30 min/day. For major CVD, when stationary time exceeded 12 h/day, risk was higher by an average of 0.13 (0.10, 0.16) per hour. Sitting time was associated with a 0.15 (0.11, 0.19) higher risk per extra hour. Time spent standing was not associated with major CVD risk.

Conclusions
Time spent standing was not associated with CVD risk but was associated with higher orthostatic circulatory disease risk. Time spent sitting above 10 h/day was associated with both higher orthostatic circulatory disease and major CVD risk. The deleterious associations of overall stationary time were primarily driven by sitting. Collectively, our findings indicate increasing standing time as a prescription may not lower major CVD risk and may lead to higher orthostatic circulatory disease risk.