bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term outcomes of apixaban as main anticoagulant in patients with HeartMate 3 left ventricular assist devices
Authors: Jdaidani Jennifer , Shadi Mahmoud , Asogwa Nnedi , Winik Jennifer , Rossi Dora , Saikus Christina , Avila Maria D. , Rojas‐Marte Geurys R. 
Published: December 2024

AbstractAimsHeartMate 3 (HM3) left ventricular assist devices (LVADs) offer improved haemocompatibility‐related outcomes for end‐stage heart failure patients, facilitating the exploration of alternative anticoagulation therapies beyond warfarin. This study presents a long‐term evaluation of thrombotic and bleeding outcomes in HM3 LVAD patients transitioned from warfarin to apixaban.MethodsWe retrospectively identified HM3 LVAD patients at our single centre who transitioned from warfarin to apixaban. Baseline characteristics were described at discharge from implant hospitalization and at the last follow‐up on each anticoagulation regimen. We reported survival, thrombo‐embolic events (including LVAD pump thrombosis, stroke, arterial thrombo‐embolic events and pump exchange) and bleeding events on both warfarin and apixaban.ResultsEight patients were identified between May 2018 and June 2022 who transitioned from warfarin to apixaban 5 mg twice daily. Patients were followed for a mean of 1233 days after LVAD implantation and 789 days after transition to apixaban. All patients were transitioned due to difficulty maintaining a therapeutic international normalized ratio (INR), including five patients who experienced bleeding complications on warfarin. No patients encountered LVAD pump thrombosis, stroke events, arterial thrombo‐embolic event, pump exchange or death. While on warfarin, five patients had eight bleeding events: one major [requiring 2 units of packed red blood cells (pRBCs)] and seven minors (five gastrointestinal bleeds, one episode of haematuria and one episode of haemoptysis). After switching to apixaban, one patient with angioectasia had a major gastrointestinal bleed requiring two pRBCs and endoscopic clipping.ConclusionsApixaban demonstrated safe and favourable long‐term outcomes in a cohort of HM3 LVAD patients over a mean follow‐up of more than 2 years. To our knowledge, our report provides the longest follow‐up duration for this patient population to date. Larger prospective studies are needed before this can be adopted as the standard of care.
Long‐term rate of heart failure in patients with autoimmune disease: A nationwide cohort study
Authors: Sun Guoli , Fosbøl Emil L. , Faurschou Mikkel , Schou Morten , Torp‐Pedersen Christian , Køber Lars , Butt Jawad H. 
Published: December 2024

ABSTRACTAimsAlthough certain autoimmune diseases (AIDs) have been associated with an increased rate of heart failure (HF), data on the long‐term rate of HF across the spectrum of AIDs are lacking. We investigated the long‐term rate of HF in individuals with a history of 28 different AIDs.Methods and resultsIndividuals diagnosed with an AID (2000–2021) were identified through Danish nationwide registries. Each patient with AID was matched with four individuals from the background population by age, sex, and year of inclusion. Multivariable Cox regression was used to compare the rate of HF between the AID and the background population, overall and according to individual AIDs. In total, 272 959 patients diagnosed with AID were matched with 1 091 836 individuals without AID (median age 55 years; 62% women; median follow‐up 7.9 years). The 10‐year cumulative incidence of HF was 5.2% for patients with AID and 3.5% for matched individuals. Patients with any AID had a higher associated rate of HF than matched individuals (hazard ratio [HR] 1.55, 95% confidence interval [CI] 1.52–1.59). Patients with each of the AIDs had a higher associated rate of incident HF compared with matched individuals from the background population, although the association was not statistically significant for Reiter's and Behcet's disease. The highest relative rates were observed in patients with systemic sclerosis (HR 3.31, 95% CI 2.63–4.16) and Addison's disease (HR 3.03, 95% CI 2.35–3.91).ConclusionPatients with AID, irrespective of the type, had a higher associated rate of HF compared to the background population. Further research is needed to clarify whether screening for cardiovascular risk is beneficial.
Effects of stocking density on growth performance, digestive enzyme activity, biochemical composition, and economic efficiency of a new strain of Oreochromis niloticus reared in cage culture system at Sindh Pakistan
Authors: Hassan Habib Ul , Ali Amjad , Wattoo Junaid , Sohail Muhammad , Raza Muhammad Ahsan , Hassan Syed Adeel , Kanwal Roohi , Kabir Muhammad , Rafiq Naseem , Manoharadas Salim , Khan Mohammad Rizwan , Arai Takaomi 
Published: December 2024

AbstractThe latest strain of Oreochromis niloticus is an altered ecological adaptation for sustainable aquaculture and is necessary to sustain stocking density and reduce physiological stress of the new strain. The present study aimed to determine the optimum stocking density, biological performance, and economic efficiency of the Nile tilapia. The 14,000 healthy seeds and uniform weight (40 ± 2.4 g) sex‐reversed Oreochromis niloticus were stocked in four cages, which are cage (1) 20 fish/m3, cage (2) 30 fish/m3, cage (3) 40 fish/m3, and cage (4) 50 fish/m3. The fish were fed 30% dietary protein and feeding frequency three times per day and the feeding rate adjusted according to the fish body weight. Results showed a significantly higher growth, weight gain, and specific growth rate in Nile tilapia stocking density on cage (1), 20 fish/m3 and cage (2), 30 fish/m3 compared to cage (3), 40 fish/m3 and cage (4), 50 fish/m3 (p < .05). The survival and growth rate showed an inverse relationship with stocking density. The feed conversion ratio (FCR) is the lowest in cage (1) and cage (2), which is significantly different from those of other cages (p < .05). The profit index (%) was significantly higher at low density. There was no significant variation in the HSI, VSI and CF. The digestive enzymes such as lipase and amylase were secreted highly in the cages (3) and (4) but high protease was secreted in cage (1). The lipid, ash, and protein of the whole fish were reduced to a lower density, but the moisture levels in the fish bodies raised significantly (p < .05) with increasing stocking density. The phenomenal regression indicates that 25–35 fish/m3 are optimum stocking density for Nile tilapia in the cage culture system. The current study has made significant step toward optimizing the stocking density of a new strain and developing cage culture in Pakistan.
Computer Folding of Parallel DNA G‐Quadruplex: Hitchhiker's Guide to the Conformational Space
Authors: Janeček Michal , Kührová Petra , Mlýnský Vojtěch , Stadlbauer Petr , Otyepka Michal , Bussi Giovanni , Šponer Jiří , Banáš Pavel 
Published: December 2024

ABSTRACTGuanine quadruplexes (GQs) play crucial roles in various biological processes, and understanding their folding pathways provides insight into their stability, dynamics, and functions. This knowledge aids in designing therapeutic strategies, as GQs are potential targets for anticancer drugs and other therapeutics. Although experimental and theoretical techniques have provided valuable insights into different stages of the GQ folding, the structural complexity of GQs poses significant challenges, and our understanding remains incomplete. This study introduces a novel computational protocol for folding an entire GQ from single‐strand conformation to its native state. By combining two complementary enhanced sampling techniques, we were able to model folding pathways, encompassing a diverse range of intermediates. Although our investigation of the GQ free energy surface (FES) is focused solely on the folding of the all‐anti parallel GQ topology, this protocol has the potential to be adapted for the folding of systems with more complex folding landscapes.
Agricultural Expansion and Landscape Heterogeneity Explain Vegetation Degradation in Brazilian Atlantic Forest Landscapes
Authors: Walder Matheus Torres , de Oliveira Carlos Leandro , Morante‐Filho José Carlos , Benchimol Maíra 
Published: December 2024

ABSTRACTSeveral anthropogenic activities in tropical forests, including deforestation and fragmentation, have led to intensive forest degradation. In fact, forest edges adjacent to anthropogenic land‐uses can be more exposed to abiotic changes and consequently lead to vegetation deterioration in forest interiors. However, there is still a lack of information on how temporal changes in land use can impact the vegetation degradation of tropical forests. Here, we investigate the influence of landscape context in explaining patterns of forest vegetation degradation over 35 years in two regions exhibiting different deforestation patterns in the threatened Atlantic Forest. Using the Normalized Difference Moisture Index (NDMI) and the Enhanced Vegetation Index (EVI), we assessed forest degradation in the center of 50 forest remnants. In particular, we estimated these indices and landscape metrics in a time series from 1985 to 2020, at a 5‐year interval, based on MapBiomas land‐use classification and Landsat imagery. Then, we used generalized linear mixed models to assess the influence of landscape metrics over time on NDMI and EVI. Our results indicated that forest degradation was intensified according to the increase in agricultural cover, although sites inserted in more heterogeneous landscapes showed reduced degradation (i.e., an increase in NDMI and EVI). We also observed that forest remnants surrounded by greater agricultural cover showed a decline in NDMI, especially in the initial years of the time series. We therefore emphasize the importance of curbing the agricultural expansion to reduce the long‐term forest degradation in Atlantic Forest remnants and suggest long‐term monitoring of forest quality using vegetation spectral indices.
Soil Microbial Assemblages and Landscape Patterns Shape Compositional Dissimilarities in Woody Plants in Urban Remnant Forest Patches
Authors: Yang Jingyi , Wang Zijin 
Published: December 2024

ABSTRACTThe effects of abiotic factors on plant composition in urban remnant forests are well‐known, while the relationships between soil microbial and plant communities in terms of compositional similarity remain unclear. In this study, we explored the relative contribution of landscape factors and soil microbial assemblages in shaping the β‐diversity of woody plants in urban remnant forest patches. Research was conducted on woody plants and soil microorganisms across 15 remnant patches in Guiyang, China. The existence of compositional similarity between soil microbial and plant assemblages in these forests was investigated. Furthermore, the study assessed the relative influence of soil microbial assemblages and landscape variables on woody plant compositions employing generalized dissimilarity models (GDMs). Findings indicate that variations in composition among woody plants are positively correlated with soil microbial communities, underscoring the vital interaction between aboveground and belowground biodiversity. The GDM results revealed that the woody plant assemblages were equally determined by both direct and indirect (via soil microbial assemblages) effects of landscape patterns, and the indirect effects were even greater than the separate direct effects. These indirect effects often surpass the direct impact of landscape features by bolstering nutrient cycling and establishing beneficial relationships between microbes and plants. Consequently, soil microbes serve as a critical bridge, transforming and amplifying the influence of landscape patterns on plant communities. Moreover, the influence of soil microbial communities and landscape patterns on the variation in woody plant compositions is modulated by their life forms. This research underscores the intertwined roles of landscape patterns and soil microbial communities in shaping plant assemblages, highlighting a dual pathway of influence—direct from landscape and indirect via soil microbes. It reveals the critical importance of considering both abiotic and biotic factors, particularly the often‐overlooked soil microbes, in ecological studies and conservation strategies.
Size Effect and Macro‐Microscopic Bearing Characteristics of Compressed Shallow Foundations Based on Discrete Element Method and Centrifugal Similarity Principle
Authors: Li Yuqi , Xu Zhichao , Ma Zhuyin 
Published: December 2024

ABSTRACTBased on the discrete element method and the centrifugal similarity theory, Particle Flow Code PFC2D was employed to establish numerical models of soil for compressed shallow foundations. The particle size effect and boundary effect of soil‐bearing capacity for compressed shallow foundations, as well as the microscopic characteristics and failure mechanisms of soil, were studied. The results show that when the ratio of the foundation width to the maximum particle size in the model was greater than or equal to 30, the effect of particle size on the soil‐bearing capacity could be ignored. When the ratio of the net distance from the foundation to the model boundary to the foundation width was greater than or equal to 2, the bearing capacity of the soil was not significantly affected by the model boundary, and the boundary effect could be ignored. With the increase in foundation width, the bearing capacity factor of the soil decreased, and the failure mode of the soil shifted from a general shear failure to a local shear failure or punching shear failure. This research in this paper not only offers valuable insights for downscaling numerical discrete element models, but also introduces novel approaches for macro‐microscopic characterization of soil‐bearing capacity.
Physics‐Informed Active Learning With Simultaneous Weak‐Form Latent Space Dynamics Identification
Authors: He Xiaolong , Tran April , Bortz David M. , Choi Youngsoo 
Published: December 2024

ABSTRACTThe parametric greedy latent space dynamics identification (gLaSDI) framework has demonstrated promising potential for accurate and efficient modeling of high‐dimensional nonlinear physical systems. However, it remains challenging to handle noisy data. To enhance robustness against noise, we incorporate the weak‐form estimation of nonlinear dynamics (WENDy) into gLaSDI. In the proposed weak‐form gLaSDI (WgLaSDI) framework, an autoencoder and WENDy are trained simultaneously to discover intrinsic nonlinear latent‐space dynamics of high‐dimensional data. Compared with the standard sparse identification of nonlinear dynamics (SINDy) employed in gLaSDI, WENDy enables variance reduction and robust latent space discovery, therefore leading to more accurate and efficient reduced‐order modeling. Furthermore, the greedy physics‐informed active learning in WgLaSDI enables adaptive sampling of optimal training data on the fly for enhanced modeling accuracy. The effectiveness of the proposed framework is demonstrated by modeling various nonlinear dynamical problems, including viscous and inviscid Burgers' equations, time‐dependent radial advection, and the Vlasov equation for plasma physics. With data that contains 5%–10 Gaussian white noise, WgLaSDI outperforms gLaSDI by orders of magnitude, achieving 1%–7 relative errors. Compared with the high‐fidelity models, WgLaSDI achieves 121 to 1779 speed‐up.
A Finite Operator Learning Technique for Mapping the Elastic Properties of Microstructures to Their Mechanical Deformations
Authors: Rezaei Shahed , Asl Reza Najian , Faroughi Shirko , Asgharzadeh Mahdi , Harandi Ali , Koopas Rasoul Najafi , Laschet Gottfried , Reese Stefanie , Apel Markus 
Published: December 2024

ABSTRACTTo obtain fast solutions for governing physical equations in solid mechanics, we introduce a method that integrates the core ideas of the finite element method with physics‐informed neural networks and concept of neural operators. We propose directly utilizing the available discretized weak form in finite element packages to construct the loss functions algebraically, thereby demonstrating the ability to find solutions even in the presence of sharp discontinuities. Our focus is on micromechanics as an example, where knowledge of deformation and stress fields for a given heterogeneous microstructure is crucial for further design applications. The primary parameter under investigation is the Young's modulus distribution within the heterogeneous solid system. Our investigations reveal that physics‐based training yields higher accuracy compared with purely data‐driven approaches for unseen microstructures. Additionally, we offer two methods to directly improve the process of obtaining high‐resolution solutions, avoiding the need to use basic interpolation techniques. The first one is based on an autoencoder approach to enhance the efficiency for calculation on high resolution grid points. Next, Fourier‐based parametrization is utilized to address complex 2D and 3D problems in micromechanics. The latter idea aims to represent complex microstructures efficiently using Fourier coefficients. The proposed approach draws from finite element and deep energy methods but generalizes and enhances them by learning parametric solutions without relying on external data. Compared with other operator learning frameworks, it leverages finite element domain decomposition in several ways: (1) it uses shape functions to construct derivatives instead of automatic differentiation; (2) it automatically includes node and element connectivity, making the solver flexible for approximating sharp jumps in the solution fields; and (3) it can handle arbitrary complex shapes and directly enforce boundary conditions. We provided some initial comparisons with other well‐known operator learning algorithms, further emphasize the advantages of the newly proposed method.
Salvage Therapy Efficacy is Modified by Risk Group at Diagnosis in Patients With Relapsed Rhabdomyosarcoma
Authors: Fetzko Stephanie , Gupta Abha A. , Setty Bhuvana A. , Malone Mary Wedekind , Schraw Jeremy , Lupo Philip J. , Russell Heidi , Nicholls Lauren , Walterhouse David , Hawkins Douglas S. , Okcu M. Fatih 
Published: December 2024

ABSTRACTBackgroundPatients with relapsed rhabdomyosarcoma (RMS) are treated with varying approaches and have a poor overall survival (OS). We performed an observational comparison of salvage regimens exploring whether high‐dose alkylator combinations were associated with longer OS.ProcedureWe categorized 110 patients with relapsed RMS from five institutions into two groups, those treated with regimens including a high‐dose alkylator (Group A) and those treated without a high‐dose alkylator (Group B). We compared OS between the two, adjusting for risk group at diagnosis and institution using Kaplan–Meier and Cox proportional hazards analyses.ResultsMedian follow‐up in the 32 survivors was 4 years (range: 1.0–16.7 years) with a 28% (95% CI: 19%–37%) 4‐year OS. Group A patients had a longer OS compared to Group B (4‐year OS 41%, 95% CI: 27%–58%, vs. 14%, 95% CI: 4%–24%, respectively, p = 0.002). Adjustment for risk group at diagnosis abrogated the association (HR 1.4, 95% CI: 0.8–2.3, p = 0.16), while controlling for institution had no effect. In stratified analyses, patients with low risk at diagnosis had the highest effect size, suggesting a benefit after high‐dose alkylator regimens (stratified HR 4.4, 95% CI: 0.96–20.3, p = 0.06, reference Group A) compared to intermediate‐ (stratified HR 1.6, 95% CI: 0.9–3.2, p = 0.13) or high‐ (stratified HR 0.9, 95% CI: 0.4–1.8, p = 0.7) risk patients.ConclusionsPatients with relapsed RMS and low‐risk group at diagnosis may benefit from high‐dose alkylator chemotherapy, while the high‐risk group has a dismal outcome regardless of treatment selection. It is inconclusive whether intermediate‐risk patients may benefit from such therapy.
Structure–activity relationships between nitrile analogues and acaricidal activities against Haemaphysalis longicornis
Authors: Lee Na‐Hyun , Lee Sangmin 
Published: December 2024

AbstractBACKGROUNDA recent increase in severe fever with thrombocytopaenia syndrome (SFTS) virus cases in Korea has been observed. This virus attacks humans and animals, and no drug is available for its treatment. This study is investigating potential control measures targeting the causative agent, Haemaphysalis longicornis.RESULTSLepidium meyenii oil was ≈8.3‐, 4.2‐ and 4.1‐fold more active than diethyltoluamide against H. longicornis larvae, nymphs and adults, respectively. The major components of L. meyenii oil were identified as benzyl nitrile (71.64%), followed by ethyl linoleic acid (13.32%), ethyl palmitate (7.81%) and 3‐methoxybenzyl nitrile (2.10%). In testing individual components of the oil were tested against H. longicornis adults, the half‐maximal lethal dose (LD50) values for benzaldehyde, benzyl nitrile and benzyl isothiocyanate were found to be 9.21, 9.19 and 18.26 μg cm−3, respectively. The acaricidal component was isolated and identified as benzyl nitrile. To establish the structure–activity relationships between nitrile analogues and acaricidal activities, benzyl nitrile (LD50: 0.56, 6.38 and 9.19 μg cm−3) exhibited the highest acaricidal activities against H. longicornis larvae, nymphs and adults, followed by benzoyl nitrile (3.24, 8.36 and 15.47 μg cm−3), phenyl nitrile (5.45, 9.35 and 17.48 μg cm−3) and diethyltoluamide (7.95, 14.81 and 22.12 μg cm−3). However, the presence of allyl, methyl or vinyl functional groups bound to the nitrile group abolished the acaricidal activity.CONCLUSIONThese results demonstrate that L. meyenii oil, benzyl nitrile, benzoyl nitrile and phenyl nitrile represent suitable options for the secure management of H. longicornis. Nevertheless, additional research is essential to develop formulations that enhance the efficacy and safety of the aforementioned acaricides. © 2024 Society of Chemical Industry.
Semi‐mechanistic population PK/PD model to aid clinical understanding of myelodysplastic syndromes following treatment with Venetoclax and Azacitidine
Authors: Thakre Neha , Maier Corinna , Zha Jiuhong , Engelhardt Benjamin , Wolff Johannes E. , Mensing Sven 
Published: December 2024

AbstractMyelodysplastic syndromes (MDS) represent a group of bone marrow disorders involving cytopenias, hypercellular bone marrow, and dysplastic hematopoietic progenitors. MDS remains a challenge to treat due to the complex interplay between disease‐induced and treatment‐related cytopenias. Venetoclax, a selective BCL‐2 inhibitor, in combination with azacitidine, a hypomethylating agent, is currently being investigated in patients with previously untreated higher‐risk MDS. We present an integrated semi‐mechanistic pharmacokinetic/pharmacodynamic (PK/PD) model developed using preliminary clinical data from an ongoing Phase 1b study evaluating the safety and efficacy of venetoclax in combination with azacitidine in treatment‐naïve patients with higher‐risk MDS. Longitudinal data from 57 patients were used to develop the model, which accounted for venetoclax PK and azacitidine treatment to describe time dynamics of bone marrow blasts, neutrophils, red blood cells, and platelets. The proliferation and maturation of progenitor cells in the bone marrow to peripheral cells is described via three parallel connected transit models including feedback terms. The model also accounted for bone marrow crowding and its impact on hematopoiesis. Model validation demonstrated adequate goodness‐of‐fit, visual and numerical predictive checks. Model predicted complete remission (CR) rates and marrow complete remission (mCR) rates closely matched observed rates in the clinical study, and simulated efficacy (recovery of blast count, CR, and mCR rates) and safety (neutropenia and thrombocytopenia) endpoints aligned with expected outcomes from various dosing regimens. Importantly, the semi‐mechanistic model may aid understanding and discriminating between disease‐driven and drug‐induced cytopenias.