bluuebunny/crossref_metadata_2025_split huggingface dataset:
Euclidean and complex geometries from real-time computations of gravitational Rényi entropies
Authors: Held Jesse , Liu Xiaoyi , Marolf Donald , Wang Zhencheng 
Published: February 2025

Abstract

Gravitational Rényi computations have traditionally been described in the language of Euclidean path integrals. In the semiclassical limit, such calculations are governed by Euclidean (or, more generally, complex) saddle-point geometries. We emphasize here that, at least in simple contexts, the Euclidean approach suggests an alternative formulation in terms of the bulk quantum wavefunction. Since this alternate formulation can be directly applied to the real-time quantum theory, it is insensitive to subtleties involved in defining the Euclidean path integral. In particular, it can be consistent with many different choices of integration contour.
Despite the fact that self-adjoint operators in the associated real-time quantum theory have real eigenvalues, we note that the bulk wavefunction encodes the Euclidean (or complex) Rényi geometries that would arise in any Euclidean path integral. As a result, for any given quantum state, the appropriate real-time path integral yields both Rényi entropies and associated complex saddle-point geometries that agree with Euclidean methods. After brief explanations of these general points, we use JT gravity to illustrate the associated real-time computations in detail.
Fine mapping and identification of causal alleles at the Ur-11 locus controlling rust resistance in common bean (Phaseolus vulgaris L.)
Authors: Erfatpour Mohammad , Simons Kristin J. , Roy Jayanta , Figueroa-Cerna Jose C. , Lee Rian , Beaver James , McClean Phillip E. , Osorno Juan M. 
Published: February 2025

Abstract
The Middle American rust resistance gene Ur-11 present in common bean (Phaseolus vulgaris L.) confers resistance to all but one known race of the pathogen Uromyces appendiculatus (Pers.) Unger. Even though progress has been made in understanding the host–pathogen interactions between common bean and U. appendiculatus, the causal alleles of the majority of rust resistance loci, including Ur-11, remain unknown. A genome-wide association study (GWAS) was conducted to identify genomic regions associated with resistance to the U. appendiculatus race 31–22, which is avirulent to Ur-11 but virulent to other Middle American rust resistance genes. GWAS using genotypic data consisting of approximately 70,959 SNP markers and phenotypic data based on the median reaction type (1–9 scale) of a panel of 357 Middle American breeding lines and cultivars, plus 5 germplasm lines with the Ur-11 locus derived from PI 181996, located Ur-11 on chromosome Pv11. Twenty-seven SNP markers clustered in the 55.16–55.56 Mb region of the P. vulgaris UI111 reference. Multiple DNA sequence alignments detected a missense mutation [c.1,328A > G] in the PvUI111.11G202400 gene model that encodes a leucine-rich repeat-containing protein in response to race 31–22. A PCR allele competitive extension marker (PACE) was developed and tested across a panel of ~ 700 Middle American dry bean genotypes. No recombination event was observed for the PACE marker among the tested genotypes; suggesting that the polymorphism on which it is based is very close to or in the Ur-11 gene. This PACE marker will be a useful and reliable marker for marker-assisted selection of Ur-11-based resistance to bean rust.
Connectivity-driven topology optimization for path-following compliant mechanism: a formulation with predictive volume constraints and adaptive strategies for gray element suppression
Authors: Zhang Lidan , Koppen Stijn , van Keulen Fred 
Published: February 2025

Abstract
We propose a topology optimization (TO) formulation and related optimization scheme for designing compliant mechanisms following a user-defined trajectory. To ensure the broad applicability and achieve precisely control of the outputs, geometric nonlinearity with incremental solutions are considered. A challenge in the design optimization of these structures is the development of formulations with satisfactory balance between (i) precise trajectory control and (ii) proper connectivity between the input/output ports and the support. Previously proposed density-based topology optimization formulations typically lack the promotion of the desired load-transferring connections, or usually complicate the design using mixed shape, size, and topology variables to enforce a minimum connectivity. To simplify design progress using exclusive topology variables, i.e., purely density-based TO methods, we propose a relatively straightforward formulation involving commonly used response functions, such as compliance and volume as constraints. For the constraints, the paper provides a scheme for defining corresponding upper limits. Numerical examples of challenging shell and plate design optimization problems demonstrate the effectiveness of the proposed formulation and scheme in the generation of load-transferring connections while limiting the impact on the performance of the path generation functionality.
Effects of a single dose of a betalain-rich concentrate on determinants of running performance and recovery muscle blood flow: a randomized, triple-blind, placebo-controlled, crossover trial
Authors: Vitti Steven , Bruneau Michael , Bisgrove Leah , Grey Samuel , Levine Sarah , Mattern Craig , Faller Justin 
Published: February 2025

Abstract

Purpose
This study aimed to examine the effects of a single dose of a betalain-rich concentrate (BRC) on determinants of running performance and recovery lactate clearance.

Methods
In this a randomized, triple-blind, placebo-controlled, crossover trial, 17 male recreational runners (Age: 19.0 ± 1.0 years; Height: 176.8 ± 6.2 cm; Weight: 70.62 ± 8.1 kg; Body fat: 12.8 ± 0.03%; VO2max: 58.9 ± 8.6 ml/kg/min) consumed an acute dose of a BRC (100 mg) or a placebo (100 mg of dextrose; CON) and performed a running economy protocol (RE) at velocities corresponding to 60% and 80% of maximal oxygen consumption (VO2max) followed by a VO2max test. Both exercise and recovery skeletal muscle oxygenation (SmO2) were assessed via near-infrared spectroscopy (NIRS), and recovery lactate was obtained.

Results
BRC resulted in lower heart rate (HR) at velocities corresponding to 80% of VO2max (p = 0.05) and maximum HR (HRmax; p = 0.01), and a lower rating of perceived exertion (RPE) at velocities corresponding to 60% of VO2max (p = 0.02) when compared to CON. BRC also improved post-exercise SmO2 at 3 (p = 0.05), 4 (p = 0.02), and 5 min (p = 0.01) but not lactate clearance (p > 0.05). BRC did not significantly improve RE or VO2max (p > 0.05).

Conclusions
A single dose of BRC did not enhance RE or VO2max. However, the observed improvements in exercise HR, RPE, and SmO₂ suggest that BRC may confer cardiovascular benefits for exercise and recovery.
Changes in internalizing and externalizing problems in Dutch children and adolescents receiving outpatient youth care before and during the COVID-19 pandemic
Authors: Broek Emma M. , De Meyer Ronald , van der Rijken Rachel , Zijlmans Josjan , van Oers Hedy A. , Luijten Michiel A. J. , Alrouh Hekmat , Popma Arne , Bartels Meike , Vermeiren Robert R. J. M. , Polderman Tinca J. C. , Tieskens Jacintha M. 
Published: February 2025

Abstract
The COVID-19 pandemic significantly impacted the mental health of children and adolescents, but its effects on treatment outcomes in youth care remain unclear. This study examines whether the pandemic influenced treatment outcomes for internalizing and externalizing problems in children receiving outpatient youth care. We analyzed data from three groups of children who received outpatient youth care (N = 1090, M

age
= 12.85): those treated entirely before the pandemic, those who transitioned into pandemic-related measures during treatment, and those treated entirely during the pandemic. The Child Behavior Checklist was used to assess internalizing and externalizing problems at the start and end of treatment. Repeated measures ANCOVAs and χ2 tests of independence were conducted to evaluate changes in problem severity and clinical status, and ANCOVAs were used to compare between-group differences. The results suggest that while overall treatment outcomes were not directly affected by the pandemic, fewer children treated during the pandemic recovered from externalizing problems compared to those treated before the pandemic. Additionally, children treated entirely during the pandemic exhibited higher levels of internalizing and externalizing problems at both the start and end of treatment, and those transitioning into the pandemic also had elevated externalizing problems at both time points. Although the pandemic did not affect the change in problems during treatment, the increased severity of issues at both the start and end of treatment indicates a deterioration in child mental health since the pandemic. Appropriate support, preventive interventions, and regular monitoring of mental health problems may mitigate future impacts.
Self-supervised learning for neural topic models with variance–invariance–covariance regularization
Authors: Xu Weiran , Hirami Kengo , Eguchi Koji 
Published: February 2025

Abstract
In our study, we propose a self-supervised neural topic model (NTM) that combines the power of NTMs and regularized self-supervised learning methods to improve performance. NTMs use neural networks to learn latent topics hidden behind the words in documents, enabling greater flexibility and the ability to estimate more coherent topics compared to traditional topic models. On the other hand, some self-supervised learning methods use a joint embedding architecture with two identical networks that produce similar representations for two augmented versions of the same input. Regularizations are applied to these representations to prevent collapse, which would otherwise result in the networks outputting constant or redundant representations for all inputs. Our model enhances topic quality by explicitly regularizing latent topic representations of anchor and positive samples. We also introduced an adversarial data augmentation method to replace the heuristic sampling method. We further developed several variation models including those on the basis of an NTM that incorporates contrastive learning with both positive and negative samples. Experimental results on three datasets showed that our models outperformed baselines and state-of-the-art models both quantitatively and qualitatively.
Clinical validation of fully automated cartilage transverse relaxation time (T2) and thickness analysis using quantitative DESS magnetic resonance imaging
Authors: Wirth Wolfgang , Herger Simon , Maschek Susanne , Wisser Anna , Bieri Oliver , Eckstein Felix , Mündermann Annegret 
Published: February 2025

Abstract

Objective
To clinically validate a fully automated cartilage segmentation technique from quantitative double-echo steady-state (qDESS) MRI supporting simultaneous estimation of cartilage T2 and morphology. Here, we test whether laminar (superficial and deep layer) T2 results from convolutional neural network (CNN) segmentations are consistent with those from manual expert segmentations.

Materials and methods
The 3D qDESS sequence was acquired using 3 T MRI (resolution: 0.3125 × 0.3125x1.5 mm) in both knees of 37 subjects with unilateral anterior cruciate ligament (ACL) injury and 48 uninjured controls. Automated femorotibial cartilage (FTJ) segmentation was based on a 2D U-Net. Laminar T2 and cartilage thickness across the FTJ) were compared between ACL-injured and contralateral knees, and between ACL-injured and control knees. Effect sizes of these differences were measured using non-parametric Cohen’s d (dn-p).

Result
Significant differences were observed only in deep T2, with longer T2 in ACL-injured knees than in contralateral and healthy control knees in most of the comparisons and with similar effect sizes for automated and manual segmentations (range dn-p automated/manual: 0.58–1.04/0.58–0.74). No significant differences were observed in superficial T2 or cartilage thickness.

Discussion
Fully-automated, CNN-based analysis showed similar sensitivity to differences in laminar cartilage T2 as manual segmentation, allowing automated qDESS-analyses to be applied to larger datasets.
Adrenocortical activity, measured via feather corticosterone, affects semen quality but not blood plasma prolactin in the capercaillie (Tetrao urogallus L.)
Authors: Sabater Alexia Siegmund , O´Brien Emma , Velázquez Rosario , Toledano-Díaz Adolfo , Castaño Cristina , Oteo Marta , de Pedro Aguilar Gabriel , Balsera Ramón , Cubero David , Łukaszewicz Ewa , Santiago-Moreno Julián 
Published: February 2025

Abstract
Capercaillie populations are experiencing worrying decline in several European countries, better knowledge of the factors affecting their reproductive success is therefore much needed. Chronic stress is a major cause of infertility in wild animals used in ex situ conservation programmes. In birds, the main hormonal stress response is an increase in corticosterone (CORT) secretion. Prolactin (PRL) is also involved, but its role in sperm functionality in birds is not well known. This work reports the relationship between CORT and PRL, and their influence on capercaillie semen quality. Feather CORT concentrations were determined by ELISA, along with blood plasma PRL by radioimmunoassay, in 14 sub-adult (1–2 years old) and 5 adult (> 3 years old) capercaillies. Sperm concentration was determined using a Neubauer chamber. Nigrosin-eosin dye was used to examine sperm viability; DNA integrity was assessed via the TUNEL assay. A significant, negative correlation was detected between CORT and sperm concentration (rs = 0.30, p = 0.02), while a positive correlation was detected between plasma PRL and DNA integrity (rs = 0.78, p = 0.007). No clear association was found between CORT and PRL (rs = 0.49, p = 0.21). These results suggest that the CORT concentration provides a suitable biomarker of stress in capercaillies, a factor known to affect reproductive function in males of this species.
Statistical Prediction of In Situ Coral Reef Carbonate Dynamics Using Endmember Chemistry, Hydrodynamic Models, And Benthic Composition
Authors: Hirsh Heidi K. , Oliver Thomas A. , Dobbelaere Thomas , Palacio-Castro Ana M. , Barkley Hannah C. , Webb Alice E. , Hanert Emmanuel , Enochs Ian C. 
Published: February 2025

Abstract
In the face of rapidly compounding climate change impacts, including ocean acidification (OA), it is critical to understand present-day stress exposure and to anticipate the biogeochemical conditions experienced by vulnerable ecosystems like coral reefs. To meaningfully predict nearshore carbonate chemistry, we must account for the complexity of the local benthic community, as well as connectivity between habitats and relevant endmember carbonate chemistry. Here, we adopt a system-scale approach to predict site-scale effects of benthic metabolism on the carbonate system of the Florida Reef Tract (FRT). We utilize bimonthly carbonate chemistry data from ten cross-shelf transects spanning 250 km of the FRT to model changes in dissolved inorganic carbon (DIC) and total alkalinity (TA). Benthic habitat maps were used to broadly classify communities known to impact carbonate chemistry. A SLIM 2D hydrodynamic model with mesh resolution reaching 100 m over reefs and along the coastline was used to determine the relevant water mass histories and identify the upstream benthic communities shaping local carbonate chemistry. These historical metabolic footprints, or “flowsheds”, were used to build predictive models of the change in DIC and TA at each station. The best predictive models included the chemical impacts of benthic ecosystem metabolism, as defined by water mass trajectories, weighted endmember chemistry, volume, time, and other environmental parameters (light, temperature, salinity, chlorophyll-a, and nitrate). Considering water mass for 5 days prior to sample collection yielded the highest model skill.
Seismic retrofit of pre-damaged RC elements using thin strain-hardening cementitious composite jackets
Authors: Ioannou Anthos I. , Pantazopoulou Stavroula J. , Petrou Michael F. , Charmpis Dimos C. 
Published: February 2025

Abstract
The emergence of cementitious materials with post-cracking strain hardening stress strain response in tension presents opportunities for retrofitting reinforced concrete elements through the application of very thin jackets, a technique that preserves the original geometry of the component. This retrofitting solution is studied experimentally in this work by replacing the damaged cover of lightly reinforced structural elements, which were previously tested under cyclic displacement reversals, simulating earthquake effects. Test specimens were detailed to represent older construction practices, where inadequate lap splicing of longitudinal reinforcement, light transverse reinforcement and thin concrete covers were common. Upon cyclic loading of the retrofitted components, the contribution of the thin jackets to the strength and deformation recovery of the old type reinforced concrete elements was examined considering the pre-existing damage. It was found that the efficacy of cover replacement with strain-hardening composites is significant not only for strength recovery but also in terms of enhanced deformability of the retrofitted component. The experimental response envelope was simulated using advanced nonlinear finite element modeling to gain improved insights regarding the stress state in the cover-replacement retrofitting layer, and to explore the performance of this retrofitting method for parameter values beyond the range of the experimental program. The amount of confinement exerted by the strain hardening cover was related to the tensile strength of the cover material and it controlled the strength recovery. However, by suppressing all brittle modes of failure along the shear span of the component, the reinforcement anchorage in the footing dominated the eventual failure mode.
Leniency experiments: an evaluation of external validity
Authors: Law Yui , Lai Sinchit , Liu Ning 
Published: February 2025

Abstract
Integrating and cross-comparing the findings of existing leniency experiments, this paper highlights multiple important experimental phenomena related to the effectiveness of leniency. The information extracted from existing leniency experiments provides useful guidelines for policy-making. In addition, this paper shows that auxiliary experimental settings may subtly influence the experimental results. Importantly, this paper explains that external validity issues are not trivial for the inferences of leniency experiments. Overlooking these external validity issues may lead to underestimation or overestimation of the effectiveness of leniency. Thus, this paper suggests that the interpretation of leniency experiments’ findings and policy recommendations should be based on relevant prior knowledge from other fields, e.g., economics, law, and psychology, as well as the theoretical and empirical studies in the field of leniency. Moreover, future leniency experiments can further enrich the understanding of this topic if existing external validity issues are addressed.
Biogeography, life strategy and ecology of Planktothrix rubescens: a review
Authors: Selmeczy Géza B. , Costa Mariana , Padisák Judit , Vasas Gábor 
Published: February 2025

Abstract

Planktothrix rubescens is a filamentous, freshwater cyanobacterium that has gained outstanding attention due to its ecological significance, toxin production capabilities and potential risks it may pose to human and environmental health. The information related to the species is fragmented in hundreds of scientific articles; thus, our main goal was to connect this knowledge, with the hope that one may uncover information that can be applied widely in the subject. This comprehensive review delves into the taxonomic classification, biogeography, environmental drivers, interaction with other species, toxin production and management strategies related to P. rubescens. The review highlights the outstanding community-forming role of the species in different environments, as well as its very complex biotic relationships, from viruses to organisms at higher trophic levels.
Investigating associations between JAK inhibition and venous thromboembolism by systematic mining of large-scale datasets
Authors: Haysen Stine Rabech , Nielsen Ane Langkilde-Lauesen , Qvist Per , Kragstrup Tue Wenzel 
Published: February 2025

Abstract
Janus kinase inhibitors (JAKi) have been associated with an increased risk of venous thromboembolism (VTE) limiting the use of JAKi-based therapy. To improve risk stratification and drug development, it is crucial to understand the implication of dysregulated JAK-Signal Transducers and Activators of Transcription (STAT) signaling in the pathogenesis of VTE. The objective of this study is to clarify the putative genomic vulnerability to dysregulated JAK–STAT signaling in VTE through systematic mining of large-scale datasets generated from studies comparing VTE patients with healthy controls. Particularly, we assess the representation of entities of the JAK–STAT signaling pathway including STAT target genes among sets of miRNA, mRNA, and proteins differentially abundant in VTE patients, and we explore the putative cumulative genetic association of JAK–STAT signaling gene sets to VTE. Genes related to the JAK–STAT pathway were found significantly altered in VTE patients compared to healthy controls, indicating that genes under transcriptional control of STAT may be dysregulated in VTE. In support of this notion, we find a significant overrepresentation of predicted STAT target genes among genes downregulated in VTE patients, and promoter sequences of differentially regulated genes were significantly enriched with STAT transcription factor binding site motifs. Further linking STAT signaling to the molecular signature of VTE, genes targeted by miRNAs differentially regulated in patients are significantly enriched with STAT target genes and genes acting in the JAK–STAT signaling pathway. Together, our findings indicate that disruptions in the JAK–STAT pathway contribute to the molecular profile of VTE. This offers hope for identifying ways to interact with the JAK–STAT pathway that do not carry the risk of VTE.