bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological and genotypic assessment of cystic echinococcosis in ruminant populations of Northern Punjab, Pakistan: a neglected zoonotic disease
Authors: Khan Sakandar , Cable Jo , Masud Numair , Hailer Frank , Younus Muhammad , Hussain Naveed , Asif Idrees Muhammad , Rashid Muhammad Imran , Akbar Haroon 
Published: January 2025

Abstract

Echinococcus
granulosus is a zoonotic dog parasite, which causes cystic echinococcosis in humans and animals, adversely affecting health and food production. The resultant socio-economic impacts in lower–middle-income countries and the paucity of epidemiology data prompted the World Health Organization to classify cystic echinococcosis as a neglected tropical disease. Between November 2019 and December 2020, the prevalence of cystic echinococcosis was assessed from 3600 post-slaughter livestock (1142 sheep, 1258 goats and 1200 buffalo) from three districts, Narowal, Sheikhupura and Sialkot, in Northern Punjab, Pakistan. The collected hydatid cysts were subjected to microscopy and PCR followed by Sanger sequencing and phylogenetic analysis. A questionnaire targeted 3600 animal owners to assess disease risk factors. Of the 28 cyst samples sequenced for mtDNA COI, the species was confirmed as Echinococcus granulosus and phylogenetic analysis revealed the presence of both G1 and G3 lineages. Overall, we noted a regional difference in prevalence, where infections were significantly higher in Sheikhupura (9.8%) than Sialkot (6.1%) or Narowal (5.9%) districts. Prevalence was higher in buffalo (9.3%) than sheep (7%) or goats (5.5%), significantly higher (9.3%) in older (> 4 years) compared to younger (< 4 years) animals (5.7%) and higher in females (9.1%) compared to males (3.8%). In sheep and buffalo, more cysts were found in the liver (77.7% and 68.7%, respectively), whereas the lungs were more commonly infected in goats (67.1%). Epidemiological data revealed that combining dog deworming with effective disposal of viscera is needed for a significant reduction in infection prevalence. Similarly, animal deworming was only associated with significantly reduced infections when the animals were not kept near an abattoir, where dogs would normally be present and feeding on discarded viscera. This study adds to growing evidence that simple public health measures and awareness are needed to reduce the prevalence of cystic echinococcosis infection.
A new approach for quantification of total above-ground heartwood and sapwood volume of trees
Authors: Arseniou Georgios , MacFarlane David W. , Raumonen Pasi 
Published: January 2025

Abstract

Key message

Terrestrial laser scanning data of trees combined with models of heartwood content proportion of woody disks can provide precise characterization of total aboveground tree sapwood and heartwood volume.

Abstract
Quantifying sapwood and heartwood content of trees is challenging. Previous studies have primarily characterized main stem wood composition, while branches have rarely been studied. Terrestrial Laser Scanning (TLS) can provide precise representations of the entire above-ground tree structure, non-destructively, to help estimate total tree sapwood and heartwood volume. In this study, we used TLS to scan above-ground portions of twenty-four open-grown, urban Gleditsia triacanthos trees on Michigan State University campus. TLS data were used to generate quantitative structure models that provided comprehensive characterizations of the total tree woody surface area (WSA) and volume. A subsample of trees was harvested (after scanning) and main stem and branch woody disks were collected to build models of heartwood content proportion. Models were applied to measurements from TLS to quantify complete heartwood and sapwood volume of each tree, including main stem and branches. From the base to the top of the trees, the largest portion of stem vertical cumulative volume was heartwood, whereas vertical cumulative volume of branches showed the opposite pattern. Absolute heartwood volume declined monotonically toward zero from stem base to stem top, while absolute sapwood volume declined sharply from stem base up to near the crown base and then remained relatively constant within crown. We also found that tree WSA increased with sapwood volume for both branches and main stem. This study developed a novel, general method for quantifying total aboveground sapwood and heartwood volume of trees and provided new insights into urban tree growth and structure.
“They knew the same struggles”: perceptions of a group coping skills intervention in patients with chronic graft-versus-host disease
Authors: Centracchio Joely A. , Yang Daniel G. , Jagielo Annemarie D. , Greer Joseph A. , El-Jawahri Areej , Traeger Lara , Nelson Ashley M. 
Published: January 2025

Abstract

Purpose
Chronic graft-versus-host-disease (cGVHD), an inflammatory condition affecting allogeneic hematopoietic cell transplantation (HCT) survivors, is associated with a range of debilitating physical and psychological sequela. Yet HCT recipients with cGVHD are virtually absent from survivorship intervention research. We conducted a randomized clinical trial to evaluate the feasibility and preliminary efficacy of a multidisciplinary group coping skills intervention (Horizons) tailored to meet these patients’ unique needs. For this follow-up qualitative analysis, we evaluated the perceived impact of the Horizons intervention by the group participants.

Methods
We purposefully selected a subset of Horizons participants (n = 19) to complete audio-recorded exit interviews via semi-structured interview guide. We used rapid analysis to characterize participant feedback in three domains: (1) motivations to participate, (2) perceived benefits of participation, and (3) impacts of participation.

Results
Findings highlight participants’ motivations to participate centered on desires to connect with others living with cGVHD and to help future patients. Perceived benefits of participation focused on the following categories: (1) connecting with other survivors, (2) learning about cGVHD, and (3) learning coping strategies to manage specific cGVHD symptoms. Impacts of participation on everyday life variably reflected categories of (1) increased sense of empowerment to contact their care team with questions and concerns, (2) increased support and validation in their struggles with cGVHD, and (3) renewed motivation or progress toward personal and health-specific goals.

Conclusion
Study findings demonstrate participants’ appreciation for a group-based opportunity to connect with others living with cGVHD and strengthen skills for navigating cGVHD challenges. Results support the ongoing need for evidence-based interventions to improve quality of life among HCT survivors.

Trial registration

www.ClinicalTrials.gov, identifier NCT04479995. Date of Registration: July 21, 2020.
The clinical effect of bone perforations in periodontal regeneration and alveolar socket preservation: a systematic review with meta-analysis
Authors: Pesce Paolo , Canullo Luigi , Testori Tiziano , Mastroianni Alessandro , Fabbro Massimo Del , Menini Maria 
Published: January 2025

Abstract

Objectives
The present systematic review aimed to evaluate if cortical bone perforation is effective in enhancing periodontal surgery and guided bone regeneration (GBR) in humans.

Materials and methods
Electronic search was performed in PubMed, Scopus and Cochrane CENTRAL up to October 31st, 2023. Grey literature was also searched. Prospective controlled studies were included. Two PICO questions were created; one focusing on the effect of bone perforation in the treatment of peridodontal intrabony defects (primary outcome probing depth (PD)) and one focusing on the effect of bone perforation in guided bone regeneration (primary outcome: histologic and histomorphometric data). The risk of bias of the included studies was assessed using the Cochrane tool for randomized controlled studies (RCTs) and the Joanna Briggs Institute Critical Appraisal tool for cohort studies. Pairwise meta-analysis was undertaken when possible, to estimate the overall effect for the outcomes investigated.

Results
The search on databases yielded a total of 653 articles. After screening, five RCTs and one non-randomized study were included. A meta-analysis was performed for the first PICO. PD was evaluated in 4 articles and no significant difference was found between the perforation vs. no perforation groups (0.11 mm (95% CI [-0.14 to 0.37 mm], P = 0.38). Additionally, radiographic defect depth (mean difference 0.77 mm, 95% CI [0.24 to 1.30 mm], P = 0.004) and distance between cemento-enamel junction and bone defect (standardized mean difference 0.98 mm, 95% CI [0.47 to 1.50 mm], P = 0.0002) resulted improved in the cortical bone perforation group.

Conclusion
The evidence supporting a positive effect of using cortical perforations is very poor. Further studies with larger sample sizes are needed to determine whether decortication brings meaningful advantages.

Clinical relevance
This study is focused on clinical studies and, using a rigorous study selection and a meta-analytic approach suggests that the apparent positive effect of bone decortication on the regeneration process still requires to be confirmed by more solid evidence.
Six years later: testing vs. model checking
Authors: Beyer Dirk , Lemberger Thomas 
Published: January 2025

Abstract
Six years ago, we performed the first large-scale comparison of automated test generators and software model checkers with respect to bug-finding capabilities on a benchmark set with 5693 C programs. Since then, the International Competition on Software Testing (Test-Comp) has established standardized formats and community-agreed rules for the experimental comparison of test generators. With this new context, it is time to revisit our initial question: Model checkers or test generators—which tools are more effective in finding bugs in software? To answer this, we perform a comparative analysis on the tools and existing data published by two competitions, the International Competition on Software Verification (SV-COMP) and Test-Comp. The results provide two insights: (1) Almost all test generators that participate in Test-Comp use hybrid approaches that include formal methods, and (2) although the considered model checkers are still highly competitive, they are now outperformed by the bug-finding capabilities of the considered test generators.
Is it worth paying attention to actinedid mites in agricultural fields?
Authors: Gergócs-Winkler Veronika , Flórián Norbert , Tóth Zsolt , Sipőcz László , Dombos Miklós 
Published: January 2025

Abstract
Agricultural management increases the seasonal dynamics of soil-dwelling organisms compared to natural habitats. Our knowledge is very poor about the relationship between seasonal changes of soil microorganisms and the microbivorous soil arthropods. To reveal these connections, we have to know more about the seasonal changes of soil-dwelling microarthropods in croplands. Actinedid mites are rarely the subject of synecological studies, however, this group regularly reaches the dominant part of mite assemblages in agro-ecosystems. In this study, we investigated the seasonal density changes of actinedid mites from two independent studies of agricultural fields. Soil samples were taken from maize and wheat fields for two years, and from newly established meadows for one year in summer and autumn in Hungary. Soil-dwelling mites were enumerated and identified at the suborder level and soil parameters were measured. Actinedid mites dominated most of our soil samples. The density of Endeostigmata was the highest in the summer and the density of Heterostigmata was the highest in the autumn within one year among different crop species, soil types, and years. Endeostigmatid mites had negative relationships with soil nitrogen parameters and positive with soil moisture. Heterostigmatid mites had various relationships with soil moisture. The ecology of actinedid mites is under-examined but their high number in agricultural fields may justify the fact that they should receive more attention. We assume that Actinedida, mainly Endeostigmata and Heterostigmata are worth to investigate in croplands as a starting point to reveal the connection between the seasonality of soil mites and soil microbiota.
Inhibition of chondroitin sulphate-degrading enzyme Chondroitinase ABC by dextran sulphate
Authors: Dalal Sagar , Pathak Rachana , Moh Edward X. S. , Packer Nicolle H. 
Published: January 2025

Abstract
Chondroitin sulphate (CS) is a sulphated glycosaminoglycan (GAG) polysaccharide found on proteoglycans (CSPGs) in extracellular and pericellular matrices. Chondroitinase ABC (CSase ABC) derived from Proteus vulgaris is an enzyme that has gained attention for the capacity to cleave chondroitin sulphate (CS) glycosaminoglycans (GAG) from various proteoglycans such as Aggrecan, Neurocan, Decorin etc. The substrate specificity of CSase ABC is well-known for targeting various structural motifs of CS chains and has gained popularity in the field of neuro-regeneration by selective degradation of CS GAG chains. Within this context, our investigation into the biochemistry of CSase ABC led us to a previously unreported inhibition of CSase ABC activity by Dextran Sulphate (DexS). To understand the inhibitory effects of DexS, we compared its inhibition of CSase ABC to that of other polysaccharides such as Heparan Sulphate, Heparin, Colominic Acid, Fucoidan, and Dextran. This analysis identified key structural factors such as monosaccharide composition and linkage, sulphation degree and overall charge as influencing CSase ABC inhibition. Remarkably, DexS emerged as a unique inhibitor of CSase ABC, with distinctive inhibitory effects that correlate with its chain length. DexS has been used to reliably induce ulcerative colitis in mice, effectively mimicking inflammatory bowel diseases in humans, and has been previously shown to inhibit both RNA polymerase and reverse transcriptase. Our investigation emphasizes the interplay between the properties of DexS and CSase ABC, providing significant insights into the utilization of polysaccharide-based inhibitors for modulating enzyme activity.
Eastward propagation of mid-latitude near-surface thermohaline anomaly and link to marine heat waves in the eastern North Pacific
Authors: Niinuma Taku , Yasuda Ichiro 
Published: January 2025

Abstract
Eastward propagations of near-surface and isopycnal thermohaline disturbances at 25.5–26.3σ
θ with a zonal speed of in-situ geostrophic current were observed in the mid-latitude (40–50° N) North Pacific and were linked to the marine heat wave (MHW) ‘The Blob’ in the Gulf of Alaska (GOA: 150–130° W and 40–50° N). Isopycnal depth anomalies were formed corresponding to wind-stress curl anomalies and propagated eastward. A warm and low-salinity disturbance was formed in the central Pacific in 2011–2012 under the negative maximum of Pacific Decadal Oscillation (PDO). This warm, low-salinity and low-density disturbance propagated eastward and was warmed by heating anomaly of surface heat flux, reduced entrainment and northward heat advection in 2013 due to the weakened westerly wind. The disturbance propagated further eastward and reached the GOA in early 2014. During the 2014–2015 MHW, heating by reduced entrainment and horizontal heat advection maintained the MHW, even though surface heat flux worked as cooling anomaly. The reduced entrainment was caused by the enhanced density stratification of the warm and low-density surface water, together with the entrainment of warm-saline subsurface water which was formed in 2013 in the area west of the GOA and subducted and propagated eastward as subsurface isopycnal warm-saline anomaly. Pycnocline heaving due to wind-induced upwelling corresponding to the strengthened Aleutian Low Pressure under the 2014–2015 El-Niño contributed to the stratification enhancement. The heating of the horizontal heat advection was due to weakened westerly wind on the northern side of strengthened and southward-shifted Aleutian Low Pressure under the El-Niño and positive PDO.
Scalable individual treatment effect estimator for large graphs
Authors: Lin Xiaofeng , Bao Han , Cui Yan , Takeuchi Koh , Kashima Hisashi 
Published: January 2025

Abstract
Causal inference plays a critical role in decision-making processes about whether to provide treatment to individuals across various domains, such as education, medicine, and e-commerce. One of the fundamental tasks in causal inference is to estimate the individual treatment effect (ITE), which represents the effect of a treatment on an individual outcome. Recently, many studies have focused on estimating ITE from graph data taking into account not only the covariates of units but also connections among them. In such a case, the outcome of a unit can be affected by not only its own covariates and treatment but also those of its neighbors, which is referred to as interference. Existing methods have utilized graph neural networks (GNNs) to capture interference and achieved improvements in estimating ITE on graph data. However, these methods are not computationally efficient and therefore cannot be applied to large graph data. To overcome this problem, we propose a novel method that reduces redundant computation in interference modeling while maintaining the prediction performance of ITE estimation. Our key idea is to model the propagation of interference by aggregating the information of neighbors before training and preserve the aggregated results for training our networks. We conduct intensive experiments on graph data consisting of up to a hundred thousand units and millions of edges. We show that the proposed method achieves superior or comparable performance to the existing GNN-based methods in ITE estimation, while the proposed method can be executed much faster than GNN-based methods.
Unmasking deception: a topic-oriented multimodal approach to uncover false information on social media
Authors: Cantini Riccardo , Cosentino Cristian , Kilanioti Irene , Marozzo Fabrizio , Talia Domenico 
Published: January 2025

Abstract
In the digital landscape, social media has emerged as a prevalent channel for global communication, connecting like-minded individuals worldwide. However, while facilitating information exchange, it is also susceptible to the dissemination of false information, posing a constant challenge to the reliability of online content. To address this issue, this paper introduces a novel methodology called TM-FID (Topic-oriented Multimodal False Information Detection), which combines false information detection and neural topic modeling within a semi-supervised multimodal approach. By jointly leveraging textual and visual information contained in online news, our approach provides insights into how false information influences specific discussion topics, thus enabling a comprehensive and fine-grained understanding of its spread and impact on social media conversation. Experimental evaluation carried out on a set of multimodal gossip-related news demonstrates the quality of the identified topics, assessed through a novel centroid-based metric, as well as the efficacy of the cross-attention mechanism used within TM-FID to accurately identify false information in multimodal news. Overall, the proposed methodology can enable effective strategies to counter the spread of false information, thereby fostering trust and confidence in the information shared on social media platforms.
Adaptive parameters identification for nonlinear dynamics using deep permutation invariant networks
Authors: Elaarabi Mouad , Borzacchiello Domenico , Bot Philippe Le , Guennec Yves L. E. , Comas-Cardona Sebastien 
Published: January 2025

Abstract
The promising outcomes of dynamical system identification techniques, such as SINDy (Brunton et al. in Proc Natl Acad Sci 113(15):3932–3937, 2016), highlight their advantages in providing qualitative interpretability and extrapolation compared to non-interpretable deep neural networks (Rudin in Nat Mach Intell 1(5):206–215, 2019). These techniques suffer from parameter updating in real-time use cases, especially when the system parameters are likely to change during or between processes. Recently, the OASIS (Bhadriraju et al. in AIChE J 66(11):16980, 2020) framework introduced a data-driven technique to address the limitations of real-time dynamical system parameters updating, yielding interesting results. Nevertheless, we show in this work that superior performance can be achieved using more advanced model architectures. We present an innovative encoding approach, based mainly on the use of Set Encoding methods of sequence data, which give accurate adaptive model identification for complex dynamic systems, with variable input time series length. Two Set Encoding methods are used: the first is Deep Set (Zaheer et al. in Adv Neural Inf Process Syst 30, 2017), and the second is Set Transformer (Lee et al. in: International conference on machine learning, PMLR, pp 3744–3753 2019). Comparing Set Transformer to OASIS framework on Lotka–Volterra for real-time local dynamical system identification and time series forecasting, we find that the Set Transformer architecture is well adapted to learning relationships within data sets. We then compare the two Set Encoding methods based on the Lorenz system for online global dynamical system identification. Finally, we trained a Deep Set model to perform identification and characterization of abnormalities for 1D heat-transfer problem.
Indication of air pollution based on the comparison of mercury and other elements in the faeces of marmots from the Western Carpathians and the Dzungarian Alatau
Authors: Haas Martina , Tomíková Katarína , Janiga Marián , Abduakassov Aibek , Kompišová Ballová Zuzana 
Published: January 2025

Abstract
The Dzungarian Alatau in Central Asia and the Western Carpathians in Central Europe are exposed to anthropogenic sources of pollution that are impacting high-altitude mountain systems through long-range transport of emissions. Based on analyses of the autumn faeces of two species of marmots (Marmota baibacina from the alpine habitats of Zhongar Alatau National Park, Marmota marmota latirostris from the alpine habitats of the Western Tatras), we determined the environmental load of mercury and other chemical elements. Our results show significantly higher levels of total mercury amounts (p < 0.0001) in faeces of marmots from the Western Tatras, Slovakia (mean = 0.066 µg/g dry weight; SD = 0.43), than in Zhongar Alatau National Park, Kazakhstan (mean = 0.034 µg/g dry weight; SD = 0.01), as well as sulphur and heavy metals (Ba, Mn, Mo, Zn, Cu, and Cr) that originate from anthropogenic activities. Other significant differences in levels of mineral nutrients (K, Cl, Ca, Fe) and Sr rather indicate differences in food sources reflecting environmental factors.