bluuebunny/crossref_metadata_2025 huggingface dataset:
LD‐informed deep learning for Alzheimer's gene loci detection using WGS data
Authors: Jo Taeho , Bice Paula , Nho Kwangsik , Saykin Andrew J. ,   Alzheimer's Disease Sequencing Project
Published: January 2025

INTRODUCTION

The exponential growth of genomic datasets necessitates advanced analytical tools to effectively identify genetic loci from large‐scale high throughput sequencing data. This study presents Deep‐Block, a multi‐stage deep learning framework that incorporates biological knowledge into its AI architecture to identify genetic regions as significantly associated with Alzheimer's disease (AD). The framework employs a three‐stage approach: (1) genome segmentation based on linkage disequilibrium (LD) patterns, (2) selection of relevant LD blocks using sparse attention mechanisms, and (3) application of TabNet and Random Forest algorithms to quantify single nucleotide polymorphism (SNP) feature importance, thereby identifying genetic factors contributing to AD risk.

METHODS

The Deep‐Block was applied to a large‐scale whole genome sequencing (WGS) dataset from the Alzheimer's Disease Sequencing Project (ADSP), comprising 7416 non‐Hispanic white (NHW) participants (3150 cognitively normal older adults (CN), 4266 AD).

RESULTS

30,218 LD blocks were identified and then ranked based on their relevance with Alzheimer's disease. Subsequently, the Deep‐Block identified novel SNPs within the top 1500 LD blocks and confirmed previously known variants, including APOE rs429358 and rs769449. Expression Quantitative Trait Loci (eQTL) analysis across 13 brain regions provided functional evidence for the identified variants. The results were cross‐validated against established AD‐associated loci from the European Alzheimer's and Dementia Biobank (EADB) and the GWAS catalog.

DISCUSSION

The Deep‐Block framework effectively processes large‐scale high throughput sequencing data while preserving SNP interactions during dimensionality reduction, minimizing bias and information loss. The framework's findings are supported by tissue‐specific eQTL evidence across brain regions, indicating the functional relevance of the identified variants. Additionally, the Deep‐Block approach has identified both known and novel genetic variants, enhancing our understanding of the genetic architecture and demonstrating its potential for application in large‐scale sequencing studies.

Highlights

Growing genomic datasets require advanced tools to identify genetic loci in sequencing.

Deep‐Block, a novel AI framework, was used to process large‐scale ADSP WGS data.

Deep‐Block identified both known and novel AD‐associated genetic loci.

rs429358 (APOE) was key; rs11556505 (TOMM40), rs34342646 (NECTIN2) were significant.

The AI framework uses biological knowledge to enhance detection of Alzheimer's loci.
Effective models for generalized Newtonian fluids through a thin porous medium following the Carreau law
Authors: Anguiano María , Bonnivard Matthieu , Suárez‐Grau Francisco J.
Published: January 2025

We consider the flow of a generalized Newtonian fluid through a thin porous medium of thickness , perforated by periodically distributed solid cylinders of size . We assume that the fluid is described by the 3D incompressible Stokes system, with a non‐linear viscosity following the Carreau law of flow index , and scaled by a factor , where . Generalizing (Anguiano M.: et al. Q. J. Mech. Math., 75(1), 1–27 (2022)), where the particular case and was addressed, we perform a new and complete study on the asymptotic behavior of the fluid as goes to zero. Depending on and the flow index , using homogenization techniques, we derive and rigorously justify different effective linear and non‐linear lower‐dimensional Darcy's laws. Finally, using a finite element method, we study numerically the influence of the rheological parameters of the fluid and of the shape of the solid obstacles on the behavior of the effective systems.
Thermal performance of DispersedInorganic magnetic hybrid nanomaterials into mixed convective flow through flexible porous disks
Authors: Faisal Muhammad , Qureshi Muhammad Zubair Akbar , Shah Nehad Ali
Published: January 2025

This study applies advanced AI techniques, including machine learning algorithms, to explore the numerically unsteady laminar flow of viscous and incompressible fluids in coaxially swirled porous disks, with applications in engineering sciences. Our focus encompasses the effects of magnetic hybrid nanomaterials and the dynamic behaviors associated with expanding/contracting and injection/suction. Utilizing single‐phase simulations, we address nonlinear coupled ordinary differential equations set against appropriate boundary conditions. Key parameters of our study include permeability and relaxation, as well as the influence of chemical reactions and mixed convection on fluid behaviors. The thermophysical properties of Al2O3/Cu nanoparticles have been by varying their morphological aspects. For the hybrid nanofluids flow, the aggregation of nanoparticle volume fraction has been designed critically in conjunction with an energy and mass transfer equation. Because dimensionless ordinary differential equations are employed, the obtained expression is transmuted using the obliging transformation technique. The desired nonlinear system of ODEs is implemented using an accurate numerical method. Our findings reveal significant impacts of chemical reaction parameters on the Sherwood number and a marked increase in the skin friction coefficient, Nusselt number, and Sherwood number as nanoparticle volume fraction rises from 2% to 7%.
Formulation of the extended plane wave expansion for in‐plane and out‐of‐plane vibrations in viscoelastic phononic thin plates under a constant temperature field
Authors: Santos Mateus C. P. dos , Filho Cimark G. Sandes , Miranda Edson J. P. de , Sinatora Amilton
Published: January 2025

In this study, we develop an extended plane wave expansion method to determine the complex elastic band gaps for both in‐plane and out‐of‐plane vibrations in a viscoelastic phononic crystal (PnC) thin plate model under a constant temperature field. The periodic structure of the thin plate comprises a unit cell (UC) consisting of an epoxy matrix and circular steel inclusions. In this configuration, we consider the viscoelastic effects described by the generalized Maxwell model arising from the epoxy matrix. Furthermore, we incorporate thermal effects in the UC, accounting for the linear dependence of the Young's modulus on the temperature of the epoxy matrix, assuming the absence of heat flow in the dimensions of the UC. We present a band structure illustrating the displacement of the real and imaginary parts of the complex band structure for evanescent waves arising from the viscoelastic PnC thin plate, considering both in‐plane and out‐of‐plane vibrations.
MHD nanofluid flow over a thin needle: Impact of second‐order slip and variable thermal properties
Authors: Bilal M. , Batool Atika , Mehmood Yasir , Ramzan M.
Published: January 2025

The complexity of second‐order slip flow phenomena demonstrated by magnetohydrodynamics (MHD) nanofluids passing through a thin needle with dynamically changing thermal characteristics is explored in this article. It delves deeply into the mutual effects of thermophoretic and Brownian motion and analyzes the implications of MHD. Specifically, temperature‐dependent variations in the viscosity and thermal conductivity of the nanofluid are observed, and the boundary contact is subject to a strict zero mass flow constraint. Employing transformative methodologies, the governing equations are transmuted into a set of intricate ordinary differential equations (ODEs), systematically tackled using the sophisticated MATLAB bvp4c algorithm to furnish precise numerical solutions. This research provides important new understandings of the complex dynamics of nanofluids surrounding thin needles, clarifying their relevance in many engineering contexts. The study reveals that the rate of heat transfer is enhanced for the higher surface needle thickness, and the fluid with higher viscosity yields a decrease in the temperature of the fluid.
On Generic Topological Embeddings
Authors: Kubiś Wiesław , Kucharski Andrzej , Turek Sławomir
Published: January 2025

We show that an embedding of a fixed 0-dimensional compact space K into the Čech–Stone remainder

$$\omega ^*$$

ω
∗

as a nowhere dense P-set is the unique generic limit, a special object in the category consisting of all continuous maps from K to compact metric spaces. Using categorical Fraïssé theory, we obtain some well-known theorems about Čech–Stone remainders of infinite discrete spaces. Furthermore, we prove several results concerning universality and homogeneity of the space

$$\kappa ^\kappa $$

κ
κ

, with

$$\kappa $$

κ

a regular uncountable cardinal, using generalized ultrametrics.
Advanced hybrid laminates: elastomer integration for optimized mechanical properties
Authors: Raimondi Luca , Bernardi Federico
Published: January 2025

Interleaving elastomeric films into polymeric composite materials is a promising technological solution to manufacture components with localized functionalities. To optimize processing time and reduce testing costs, there is an urgent need for modeling strategies to predict the effect of hybridization based on the fundamental properties of singular constituents. In this work, three different laminates with varying numbers and positions of elastomeric layers were manufactured and mechanically tested in flexural configuration. The digital image correlation (DIC) technique is employed to evaluate the displacements and the strain field on the surface of the sample. A numerical framework for the prediction of the mechanical response, including damage initiation and evolution, was developed and validated against experimental data. The numerical results showed significant agreement with the experiments, reporting a maximum mismatch of about 10% in strain distribution and about 2% in the ultimate load. Additionally, degradation trends in the load vs. deflection curves were always consistent. Analysis of the fractured surface and predicted failure modes further demonstrated the reliability of the method.
A metal 3D-printed non-assembly mandrel for profile bending
Authors: Kotzian Tobias , Frohn-Sörensen Peter , Nebeling Daniel , Engel Bernd
Published: January 2025

In the overall regime of production technologies, bending processes allow production of complex parts and profiles in a precise, flexible, and economical way. It is important to manufacture tools which are universally applicable and easy to manufacture, since modern industries demand flexibility in terms of larger varieties or smaller batch sizes. In the past, it was difficult and time-consuming to manufacture bending tools, especially mandrels, due to their high geometric complexity and tight assembly of swivel joints. In this paper, we present a new design approach for the bending mandrel which is suitable for metal additive manufacturing that incorporates non-assembly mechanisms of joints. The hinges are systematically developed with particular focus on achieving a minimized gap and resultant clearance. As a test case, a mandrel is 3D printed by using the laser powder bed fusion technique and successfully tested in the rotary draw bending process parameterized for narrow bends in stainless steel tubes. In the light of these results, a solution is formulated for ease in manufacturing and faster rate of tool production, in this case bending mandrel. This methodology facilitates the production of small batch sizes and large product variants in bending processes. The research presented in this paper serves as a forward step towards economical production of complex parts in a highly flexible manner.
Percolation for 2D Classical Heisenberg Model and Exit Sets of Vector Valued GFF
Authors: Aru Juhan , Garban Christophe , Sepúlveda Avelio
Published: January 2025

Our motivation in this paper is twofold. First, we study the geometry of a class of exploration sets, called exit sets, which are naturally associated with a 2D vector-valued Gaussian Free Field :

$$\phi : \mathbb {Z}^2 \rightarrow \mathbb {R}^N, N\ge 1$$

ϕ
:

Z

2

→

R

N

,
N
≥
1

. We prove that, somewhat surprisingly, these sets are a.s. degenerate as long as

$$N\ge 2$$

N
≥
2

, while they are conjectured to be macroscopic and fractal when

$$N=1$$

N
=
1

. This analysis allows us, when

$$N\ge 2$$

N
≥
2

, to understand the percolation properties of the level sets of

$$\{ \Vert \phi (x)\Vert _{{2}}, x\in \mathbb {Z}^2\}$$

{
‖
ϕ

(
x
)

‖
2

,
x
∈

Z

2

}

and leads us to our second main motivation in this work: if one projects a spin

$$O(N+1)$$

O
(
N
+
1
)

model (the case

$$N=2$$

N
=
2

corresponds to the classical Heisenberg model) down to a spin O(N) model, we end up with a spin O(N) in a quenched disorder given by random conductances on

$$\mathbb {Z}^2$$

Z

2

. Using the exit sets of the N-vector-valued GFF, we obtain a local and geometric description of this random disorder in the limit

$$\beta \rightarrow \infty $$

β
→
∞

. This allows us in particular to revisit a series of celebrated works by Patrascioiu and Seiler (J Stat Phys 69(3):573–595, 1992, Nucl Phys B Proc Suppl 30:184–191, 1993, J Stat Phys 106(3):811–826, 2002) which argued against Polyakov’s prediction that spin

$$O(N+1)$$

O
(
N
+
1
)

model is massive at all temperatures as long as

$$N\ge 2$$

N
≥
2

(Polyakov in Phys Lett B 59(1):79–81, 1975). We make part of their arguments rigorous and more importantly we provide the following counter-example: we build ergodic environments of (arbitrary) high conductances with (arbitrary) small and disconnected regions of low conductances in which, despite the predominance of high conductances, the XY model remains massive. Of independent interest, we prove that at high

$$\beta $$

β

, the fluctuations of a classical Heisenberg model near a north pointing spin are given by a

$$N=2$$

N
=
2

vectorial GFF. This is implicit for example in Polyakov (1975) but we give here the first (non-trivial) rigorous proof. Also, independently of the recent work Dubédat and Falconet (Random clusters in the villain and xy models, arXiv preprint arXiv:2210.03620, 2022), we show that two-point correlation functions of the spin O(N) model can be given in terms of certain percolation events in the cable graph for any

$$N\ge 1$$

N
≥
1

.
Morphological analysis of inosculated connections in weeping figs: insights on density, geometry, fiber structures, and compositional variations
Authors: Wang Xiuli , Gard Wolfgang , Mosleh Yasmine , van de Kuilen Jan-Willem
Published: January 2025

Trees exhibit adaptability in response to external loads, which allows them to form an inosculated connection (self-growing connection) with a neighboring tree. Such connections have the mechanical potential to build living tree structures. Although qualitative studies have studied this phenomenon, quantitative analysis of its growth features remains limited. Self-growing connections fused by weeping figs (Ficus benjamina L.) are utilized to study growth features. X-ray scanning and optical microscopy techniques are employed to investigate parameters including density, geometry, fiber structures, and material compositions. Key findings demonstrate that the fused region of a connection has a larger volume and a higher density on the intersected surface. Microscopic analysis identifies that the enlarged wood in the fused area is tension wood characterized by G-layers. The key component that connects trees is referred to as merged fibers, and the pattern of their distribution is found to be mainly in the outer layer of the larger cross-angle of a connection. At the cellular level, crystals within cells are identified in the fused region, implying possible mechanical stresses the interface has experienced. The findings in self-growing connections can serve as inspiration for structural design in living structures, biomimicry, bioinspired structures, and advancements in bioeconomics.
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

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

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.

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

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

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

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

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

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

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

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

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

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

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.
Restoring populations of Populus pruinosa Schrenk through biotechnology
Authors: Turdiyev Timur , Kovalchuk Irina , Madenova Aigul , Kuan Angsagan , Mikhailenko Natalya , Kabylbekova Balnur , Baizhumanova Saule , Yemesheva Kamila , Tuigunov Zakir , Rakhimbayev Izbassar
Published: January 2025

The most effective method to combat desertification is planting artificial forests of Populus pruinosa. In the Zhetysu and Almaty regions, samples were gathered from natural stands, which P. pruinosa and P. diversifolia likely displaced. The morphological attributes of 27 samples were related to one species, but one sample was causing doubt. PCR analyses were performed using eight microsatellite markers. The genotyping results revealed that all of the 28 samples collected were of the same type of P. pruinosa. They can effectively be introduced into in vitro culture in winter when physiological dormancy has ended. Annual lignified cuttings 6 to 7 cm long with 1 to 2 buds from selected plus trees were sterilized from saprophytic microflora by bleach NaOCl (1:1) for 10 min and 0.1% HgCl2 solution for 5 min and placed on the medium. Both male and female plants were propagated in the medium that contained ½ Murashige and Skoog (MS), 0.1 mg L-1 BAP; 0.02 mg L-1 GA; 20 g L-1 Glucose; pH 5.7, where the multiplication rate averaged 3.8 to 4.5, and the shoot length at 5.7 to 7.0 cm in 4 to 6 wk. For the transferring regenerated plants to soil in pots, the best substrate was found as peat, humus, and sand at a ratio of 50:40:10, respectively.
Life as a Design Element of Hardened Urban Shorelines
Authors: Grothues Thomas M. , Padilla Dianna K. , Kolatan Sulan , Kaunzinger Christina M. K. , Parker Philip , Handel Steven N.
Published: January 2025

Armored urban shorelines have historically impoverished life on the waterfront. Materials and forms were chosen to discourage the settlement of marine communities and human access. This has weakened shoreline habitats and adjacent terrestrial and aquatic ecosystems and diminished urban human experiences by reducing links to nature. Augmentation of existing structures and new waterfront designs for specific ecological goals such as salmon habitat improvement are reversing these trends. With the integration of advances in ecology, social science, engineering, architecture, and regulation, urban shorelines can be designed and built to enrich human experience and natural resources through connections rather than through separation and can then be considered “living shorelines.” Such a holistic approach should extend from the subtidal to the terrestrial vegetated and built environment. As with traditional soft sediment living shorelines, life can be included from the outset and be applied as an integral design element providing many functions as well as ecosystem services and social well-being benefits. We present challenges and recommend solutions for broad incorporation of this new vision for urban shorelines. We need data on biological recruitment processes, a better understanding of human social engagement with the urban shore, and continued development of materials for strength, customizability, ecosystem compatibility, and reduced carbon footprint. Measuring and tracing impacts or contributions will be difficult. Improved assessments of investment risk and reward for urban areas are needed to fund these efforts, and regulatory adaptability is needed to allow the transformation of urban shores into living shores.
In situ alloying of AlCuSi using dual-wire-directed energy deposition with plasma
Authors: Reinbacher S. , Klein T. , Simson C. , Warchomicka F. , Spoerk-Erdely P. , Enzinger N.
Published: January 2025

The current research explores additive manufacturing of a multi-phase material using dual-wire plasma-directed energy deposition technology. With this approach, new materials can be designed and tested easily on the basis of commercially available consumables. In this work, AlSi5 and CuAl8 solid wire consumables are used to produce a specific AlCuSi alloy by controlling the welding parameters and the wire feed ratio. Initial experimentation results in an alloy with 85.7 at.% aluminum, 8.4 at.% copper, 2.7 at.% silicon, and 3.2 at.% magnesium, but with some instabilities during the process. The presence of magnesium in the chemical composition could be related to plasma interaction with the substrate during the welding process. After optimizing the process parameters, the chemical composition obtained is about 76.3 at.% aluminum, 19.9 at.% copper, and 3.8 at.% silicon. Using microstructural analysis via light and scanning electron microscopy, defects such as pores and inadequately melted Cu wire material are observed in all materials produced. Although the optimization of the melting process improved the microstructure, it also increased the copper content, which in turn exerts a significant influence on the mechanical properties. Mechanical testing indicates significant embrittlement. The results underscore that the microstructure is heavily influenced by the chemical composition. Microstructural changes caused by the higher copper content, i.e., in particular the increase of the volume fraction of brittle intermetallic phases such as θ-Al2Cu, result in severe embrittlement of the obtained materials, denoted by higher hardness and reduced toughness. We conclude that the use of dual-wire plasma additive manufacturing can develop new materials by in situ alloying.
Erwachsenenerziehung durch Sachbücher?
Authors: Nohl Arnd-Michael
Published: January 2025

Angesichts der aktuellen gesellschaftlichen Herausforderungen ist zu fragen, ob die pädagogische Ergänzung politischer Entscheidungen sich allein auf die Bildung Erwachsener stützen kann oder ob nicht auch erzieherische Formate notwendig sind. Diese stehen allerdings unter einem Entmündigungsverdacht. Einen Ausweg aus diesem Dilemma könnten Sachbücher mit einem erzieherischen Impetus bieten. Exemplarisch werden daher Sachbücher, die ihren Leserinnen und Leser rassismuskritische Sichtweisen unterbreiten und sie z. T. zu diesen erziehen, interpretiert. Deutlich werden hier nicht nur unterschiedliche pädagogische Adressierungen der Leserinnen und Leser, die vom Bildungsangebot bis zu inszenierten Erziehungsprozessen reichen, sondern auch neue Perspektive auf die Entmündigungsproblematik.
The Effect of Boric Acid on Oxidative Stress, Inflammation, and Apoptosis in Embryonic and Fetal Tissues Damage Caused by Consumption of High-Fructose Corn Syrup in Pregnant Rats
Authors: Başeğmez Mehmet , Yüksel Duygu
Published: January 2025

This study aimed to determine the protective role of boric acid in a pregnant rat model of high fructose corn syrup consumption. Consumption of high fructose corn syrup has been associated with adverse health outcomes in humans and animals. Twenty-eight healthy female Wistar albino rats (250–300 g weight and 16–24 weeks old) were randomly distributed into four equal groups (n = 7): Control, Boric acid (BA), High Fructose Corn Syrup (HFCS), HFCS + BA. Boric acid (20 mg/kg) was administered to pregnant rats via oral gavage every day during pregnancy. The prepared 30% HFCS (F30) solution (24% fructose, 28% dextrose) was added to the drinking water throughout pregnancy. At the end of pregnancy (day 19), blood, placenta, uterus, and fetuses were collected from rats. The results indicated that HFCS increases oxidative stress by increasing the level of MDA and decreasing GSH, SOD, and CAT activity in the blood of maternal. However, BA administration significantly decreased MDA levels and increased GSH levels, SOD, and CAT activity (p < 0.05). In addition, HFCS consumption significantly increased plasma TNF-α, IL-6, and leptin levels compared to control, BA, and HFCS + BA groups (p < 0.05). However, BA administration significantly decreased plasma TNF-α, IL-6, and leptin levels (p < 0.05). Furthermore, BA (20 mg/kg) significantly decreased HFCS-induced histopathological and immunohistochemical alterations in the placenta, uterus, and fetal tissue. In conclusion, BA may prevent HFCS toxicity in maternal and fetal tissues, as it regulates oxidative imbalance in pregnant rat and alleviates histopathological and immunohistochemical changes. The findings indicate a need for further studies to assess the potential of boron in preventing or mitigating the effects of HFCS during pregnancy.

Graphical Abstract
Improving the reproducibility in geoscientific papers: lessons learned from a Hackathon in climate science
Authors: Coca-Castro Alejandro , Fouilloux Anne , Barros Lourenço Ricardo , McDonald Andrew , Rao Yuhan , Hosking J. Scott
Published: January 2025

In this paper, we explore the crucial role and challenges of computational reproducibility in geosciences, drawing insights from the Climate Informatics Reproducibility Challenge (CICR) in 2023. The competition aimed at (1) identifying common hurdles to reproduce computational climate science; and (2) creating interactive reproducible publications for selected papers of the Environmental Data Science journal. Based on lessons learned from the challenge, we emphasize the significance of open research practices, mentorship, transparency guidelines, as well as the use of technologies such as executable research objects for the reproduction of geoscientific published research. We propose a supportive framework of tools and infrastructure for evaluating reproducibility in geoscientific publications, with a case study for the climate informatics community. While the recommendations focus on future CIRCs, we expect they would be beneficial for wider umbrella of reproducibility initiatives in geosciences.