bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust contact-constrained topology optimization considering uncertainty at the contact support
Authors: Schmidt Timo , Kriegesmann Benedikt , Seifried Robert 
Published: March 2024

AbstractIn this paper, the general framework for contact-constrained topology optimization of Strömberg and Klarbring (2010) is extended to robust topology optimization. In doing so, a linear elastic design domain is considered and the augmented Lagrangian approach is used to model the unilateral contact. For topology optimization, the design space is parametrized with the SIMP-approach and the Sigmund’s filter is applied. Additionally, the robust framework considers uncertainties at the contact support such as deviations of the geometry of the contact surface and the friction coefficient. Both uncertainties are described by the first-order second-moment method which leads to minimal additional costs. In fact, only two additional linear equations must be solved to obtain the robust objective and its gradient with respect to the design variables. Having both the objective and the gradient, the design update is computed with the method of moving asymptotes. The robust framework is applied to 2D and 3D examples to prove its scalability for real-world applications.
Topography optimisation using a reduced-dimensional model for transient conjugate heat transfer between fluid channels and solid plates with volumetric heat source
Authors: Sun Yupeng , Yao Song , Alexandersen Joe 
Published: March 2024

AbstractConsideration of transient effects is important for industrial applications of heat transfer structure optimisation studies; however, the huge computational cost associated with transient problems is a pressing concern. This paper proposes an extension of a previous reduced-dimensional model to transient conjugate heat transfer between a fluid flow and solid-heated plates in a plate heat exchanger. The extended reduced-dimensional model introduces the temperature field of the plate governed by the heat conduction equation, which is coupled to the temperature field of the fluid, governed by the convection-diffusion equation, through the heat flux balance equation at the contact surface. The model is based on assumptions of fully developed flow and constant temperature profile, reducing the three-dimensional problem to a planar problem and significantly reducing computational costs. The accuracy of the model for the simulation of transient heat transfer is verified by comparison with a three-dimensional model. In this paper, the topography of the heat exchanger plate is optimised for both steady-state and transient conditions by applying the reduced-dimensional model. The effectiveness of the optimised design was demonstrated by the cross-check of both the reduced-dimensional and full three-dimensional models. Furthermore, this work considers the effect of time-independent boundary conditions and time-dependent boundary conditions on transient optimisation. The transient and steady-state optimised designs are analysed and compared for both conditions, and the necessity of transient optimisation is discussed.
Involvement of per- and polyfluoroalkyl compounds in tumor development
Authors: Pesonen Maija , Vähäkangas Kirsi 
Published: March 2024

AbstractPer- and polyfluoroalkyl substances (PFAS) are a large group of synthetic persistent chemicals, which are used in many industrial and commercial applications. Hundreds of different PFAS have been identified in the environment and they are commonly found also in human blood. Due to the chemical stability and extensive use, PFAS pose a risk for human health and wildlife. Mounting evidence indicates that PFAS-exposure adversely affects many organs including liver, kidney, and reproductive tissues and induces tumors in laboratory rodents. Epidemiological studies show association between PFAS-exposure and some tumors also in humans. Effects of PFAS-exposure are complex and obviously do not depend only on the concentration and the structure of PFAS, but also on age and sex of the exposed individuals. It has been difficult to show a causal link between PFAS-exposure and tumors. Moreover, molecular mechanisms of the PFAS effects in different tissues are poorly understood. PFAS are not directly mutagenic and they do not induce formation of DNA binding metabolites, and thus are assumed to act more through non-genotoxic mechanisms. In this review, we discuss the involvement of PFAS-compounds in tumor development in tissues where PFAS exposure has been associated with cancer in epidemiological and animal studies (liver, kidney, testicle and breast). We will focus on molecular pathways and mechanisms related to tumor formation following PFAS-exposure.
Recent advances and current challenges of new approach methodologies in developmental and adult neurotoxicity testing
Authors: Serafini Melania Maria , Sepehri Sara , Midali Miriam , Stinckens Marth , Biesiekierska Marta , Wolniakowska Anna , Gatzios Alexandra , Rundén-Pran Elise , Reszka Edyta , Marinovich Marina , Vanhaecke Tamara , Roszak Joanna , Viviani Barbara , SenGupta Tanima 
Published: March 2024

AbstractAdult neurotoxicity (ANT) and developmental neurotoxicity (DNT) assessments aim to understand the adverse effects and underlying mechanisms of toxicants on the human nervous system. In recent years, there has been an increasing focus on the so-called new approach methodologies (NAMs). The Organization for Economic Co-operation and Development (OECD), together with European and American regulatory agencies, promote the use of validated alternative test systems, but to date, guidelines for regulatory DNT and ANT assessment rely primarily on classical animal testing. Alternative methods include both non-animal approaches and test systems on non-vertebrates (e.g., nematodes) or non-mammals (e.g., fish). Therefore, this review summarizes the recent advances of NAMs focusing on ANT and DNT and highlights the potential and current critical issues for the full implementation of these methods in the future. The status of the DNT in vitro battery (DNT IVB) is also reviewed as a first step of NAMs for the assessment of neurotoxicity in the regulatory context. Critical issues such as (i) the need for test batteries and method integration (from in silico and in vitro to in vivo alternatives, e.g., zebrafish, C. elegans) requiring interdisciplinarity to manage complexity, (ii) interlaboratory transferability, and (iii) the urgent need for method validation are discussed.
Isomerization pathway of a C–C sigma bond in a bis(octaazamacrocycle)dinickel(II) complex activated by deprotonation: a DFT study
Authors: Jelemenska Ingrid , Zalibera Michal , Rapta Peter , Dobrov Anatoly A. , Arion Vladimir B. , Bucinsky Lukas 
Published: March 2024

AbstractThe anti (a) to syn (s) isomerization pathway of the deprotonated form of the dimer with two nickel(II) 15-membered octaazamacrocyclic units connected via a carbon–carbon (C–C) σ bond was investigated. For the initial anti (a) structure, a deprotonation of one of the bridging (sp3 hybridized) carbon atoms is suggested to allow for an a to s geometry twist. A 360° scan around the bridging C–C dihedral angle was performed first to find an intermediate geometry. Subsequently, the isomerization pathway was explored via individual steps using a series of mode redundant geometry optimizations (internal coordinates potential energy surface scans) and geometry relaxations leading to the s structure. The prominent geometries (intermediates) of the isomerization pathway are chosen and compared to the a and s structures, and geometry relaxations of the protonated forms of selected intermediates are considered.
Assessment of pelvic organ prolapse with the Pelvic Inclination Correction System: defining the normal range and threshold to pathology
Authors: Ghafoor Soleen , Beintner-Skawran Stephan , Betschart Cornelia , Winklehner Thomas , Reiner Cäcilia S. 
Published: March 2024

Abstract
Purpose
To define the normal range and threshold values for pathologic prolapse on MRI using the PICS line and assess its correlation with the pubococcygeal line (PCL).

Methods
This prospective, IRB-approved study included 20 nulliparous volunteers and 18 prolapse patients (POP-Q Stage ≥ 2). Organ positions (bladder, cervix, anorectal junction) relative to PICS and PCL were measured on dynamic MRI. Differences in organ position were compared. Receiver-operating characteristic (ROC) analysis was performed to identify cutoff values for prolapse using the PICS line. The correlation between PICS and PCL measurements was tested with Spearman’s rank correlation.

Results
In volunteers, median bladder and cervix positions measured to the PICS at rest were − 2.7 cm and − 5.3 cm compared to − 1.9 cm and − 2.7 cm in patients (p < 0.001). During straining, bladder and cervix were at − 0.9 cm and − 3.2 cm in volunteers versus + 2.5 cm and + 2.5 cm in patients (p < 0.001). Correlation was strong for PICS and PCL measurements for all three compartments (δ = 0.883–0.970, p ≤ 0.001). AUCs of PICS for the anterior and middle compartment were 0.98 (95% confidence interval [CI] 0.96–1.00, p < 0.001) and 0.96 (95% CI 0.89–1.00, p < 0.001) for differentiating patients from healthy volunteers. AUC for the posterior compartment was 0.76 (95% CI 0.57–0.96, p = 0.034).

Conclusion
PICS measurements reliably differentiate patients from volunteers in the anterior and middle compartment. Future studies need to identify a reliable threshold for the posterior compartment. PICS and PCL measurements are strongly correlated.

Graphical abstract
Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation
Authors: Miloro Fabio , Kis András , Havelda Zoltán , Dalmadi Ágnes 
Published: March 2024

Abstract
Key message
Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5′ terminal nucleotide of small RNAs, demonstrating functional conservation and divergence.

Abstract
The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5′ adenine residue, while also accepting 5′ guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5′ adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.
Cost-effectiveness of quality improvement intervention to reduce time between CT-detection and ureteroscopic laser fragmentation in acute symptomatic ureteric stones management
Authors: Khopekar Faid , Nabi Soha , Shiva Mehdi , Stewart Morven , Rajendran Benedict , Nabi Ghulam 
Published: March 2024

Abstract
Objective
To prospectively assess clinical and cost effectiveness of emergency ureteroscopic laser fragmentation of urinary stones causing symptoms or obstruction.

Patients and methods
100 consecutive patients with an average (median) age 55.6 (57.5) years and average (median) stone size of 8.2 mm (± 7 mm) between October 2018 and December 2021 who underwent emergency ureteroscopy and laser fragmentation formed the study cohort as part of a clinical service quality improvement. Primary outcome was single procedure stone-free rate and cost-effectiveness. The secondary outcomes were complications, re-admission and re-intervention. A decision analysis model was constructed to compare the cost-effectiveness of emergency ureteroscopy with laser fragmentation (EUL) and emergency temporary stenting followed by delayed ureteroscopy with laser fragmentation (DUL) using our results and success rates for modelling.

Results
Single procedure stone-free rates (SFR) for EUL and DUL were 85%. The re-intervention rate, re-admission and complication rates of the study cohort (EUL) were 9%, 18%, and 4%, respectively, compared to 15%, 20%, and 5%, respectively for the control cohort (DUL). The decision analysis modelling demonstrated that the EUL treatment option was more cost-efficient, averting £2868 (€3260) per patient for the UK health sector. Total cost of delayed intervention was £7783 (€8847) for DUL in contrast to £4915 (€5580) for EUL.

Conclusions
Implementation of quality improvement project based on a reduction in CT detection-to-laser fragmentation time interval in acute ureteric obstruction or symptoms caused by stones had similar clinical effectiveness compared to delayed ureteroscopic management, but more cost-effective.
Ureteral wall thickness as a predictor for non-invasive treatment success for steinstrasse. Can we save time?
Authors: Elbaset M. A. , Taha Diaa-Eldin , Anas Marwan , Elghareeb Ahmed , Abouelkheir Rasha T. , Ashour Rawdy , Sheir K. Z. , Osman Yasser 
Published: March 2024

Abstract
Purpose
We aimed to define factors affecting the non-invasive overall treatment success (medical expulsive therapy (MET) ± shock wave lithotripsy (SWL)) for uncomplicated ureteral steinstrasse (SS) clearance.

Methods
We retrospectively evaluated consecutive patients who underwent SWL for renal stones between 2017 and 2021. Patients with uncomplicated SS were included. All patient’s demographic and radiological data, e.g., age, gender, pre-SWL stenting, SS site, type, leading stone size in widest diameter (< 10 mm and ≥ 10 mm), ureteral wall thickness (UWT) in mm against the leading stone were collected. If SS was diagnosed, medical treatment was given for 4 weeks. In case of MET failure, either SWL for the leading stones + MET or direct URS was done. Non-invasive treatment success (SFR) was considered if complete clearance of SS occurred with no complications or the need for invasive intervention.

Results
A total of 145 patients were included with mean age of 45.9 ± 12.4 years. SFR in case of MET only occurred in 27.9%. Complications happened in 26 patients (17.9%). Non-invasive treatment SFR was achieved in 78 patients (53.8%) totally where SS type I, leading stone size ≤ 10 mm type and decreased UWT around the leading stone increased treatment success.

Conclusion
Ureteral wall thickness is an important factor predicting SS management success. Besides the decreased UWT, non-invasive management should be offered for type I SS with leading stone ≤ 10 mm.
CurveML: a benchmark for evaluating and training learning-based methods of classification, recognition, and fitting of plane curves
Authors: Raffo Andrea , Ranieri Andrea , Romanengo Chiara , Falcidieno Bianca , Biasotti Silvia 
Published: March 2024

AbstractWe propose CurveML, a benchmark for evaluating and comparing methods for the classification and identification of plane curves represented as point sets. The dataset is composed of 520k curves, of which 280k are generated from specific families characterised by distinctive shapes, and 240k are obtained from Bézier or composite Bézier curves. The dataset was generated starting from the parametric equations of the selected curves making it easily extensible. It is split into training, validation, and test sets to make it usable by learning-based methods, and it contains curves perturbed with different kinds of point set artefacts. To evaluate the detection of curves in point sets, our benchmark includes various metrics with particular care on what concerns the classification and approximation accuracy. Finally, we provide a comprehensive set of accompanying demonstrations, showcasing curve classification, and parameter regression tasks using both ResNet-based and PointNet-based networks. These demonstrations encompass 14 experiments, with each network type comprising 7 runs: 1 for classification and 6 for regression of the 6 defining parameters of plane curves. The corresponding Jupyter notebooks with training procedures, evaluations, and pre-trained models are also included for a thorough understanding of the methodologies employed.
Ocean response to a century of observation-based freshwater forcing around Greenland in EC-Earth3
Authors: Devilliers Marion , Yang Shuting , Drews Annika , Schmith Torben , Olsen Steffen M. 
Published: March 2024

AbstractThe acceleration of Greenland ice sheet melting over the past decades is raising concern regarding the impacts on ocean circulation in the North Atlantic and Arctic regions. Global climate models struggle to assess these impacts as they do not include a realistic amount of meltwater from the Greenland ice sheet. Using an extended observation-based dataset of runoff and solid ice discharge for the recent historical period (1920–2019), we force the EC-Earth3 climate model following the ensemble approach and protocol of a previous study using a different model. We observe a slight increase of the ensemble mean AMOC with a large spread in the response: $$0.20\pm 0.81$$

0.20
±
0.81

Sv for the maximum AMOC at 45$$^{\circ }$$

∘

N. We notice that members with a strong initial AMOC state (18 Sv) show a strengthening of the AMOC, while members with intermediate AMOC strength between 16 and 18 Sv are not affected by the freshwater forcing. Weaker initial AMOC members respond with a mean weakening of $${-}\,0.21\pm 0.58$$

-

0.21
±
0.58

Sv of the AMOC. The AMOC ensemble spread is reduced by half in the freshwater forced ensemble at the end of the experiment and the negative trend is stronger compared to historical simulations without the forcing. This suggests the possible ability of the freshwater to constrain AMOC variability on multi-decadal time-scales. Comparison of the two ten member ensembles with ORAS5 reanalysis shows a reduction of the surface temperature and salinity biases in the freshwater forced ensemble in key regions such as the North Atlantic subpolar gyre and the Beaufort Gyre relative to the historical simulations. Recent trends are also more aligned with reanalysis in those regions. Arctic Ocean Atlantic Water subsurface core temperature is also closer to reanalysis but still strongly biassed. Members with a high AMOC initial state display an unrealistic Atlantic water layer core depth.
Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia
Authors: Marques Christine , Held Aaron , Dorfman Katherine , Sung Joon , Song Catherine , Kavuturu Amey S. , Aguilar Corey , Russo Tommaso , Oakley Derek H. , Albers Mark W. , Hyman Bradley T. , Petrucelli Leonard , Lagier-Tourenne Clotilde , Wainger Brian J. 
Published: March 2024

AbstractThe stimulator of interferon genes (STING) pathway has been implicated in neurodegenerative diseases, including Parkinson’s disease and amyotrophic lateral sclerosis (ALS). While prior studies have focused on STING within immune cells, little is known about STING within neurons. Here, we document neuronal activation of the STING pathway in human postmortem cortical and spinal motor neurons from individuals affected by familial or sporadic ALS. This process takes place selectively in the most vulnerable cortical and spinal motor neurons but not in neurons that are less affected by the disease. Concordant STING activation in layer V cortical motor neurons occurs in a mouse model of C9orf72 repeat-associated ALS and frontotemporal dementia (FTD). To establish that STING activation occurs in a neuron-autonomous manner, we demonstrate the integrity of the STING signaling pathway, including both upstream activators and downstream innate immune response effectors, in dissociated mouse cortical neurons and neurons derived from control human induced pluripotent stem cells (iPSCs). Human iPSC-derived neurons harboring different familial ALS-causing mutations exhibit increased STING signaling with DNA damage as a main driver. The elevated downstream inflammatory markers present in ALS iPSC-derived neurons can be suppressed with a STING inhibitor. Our results reveal an immunophenotype that consists of innate immune signaling driven by the STING pathway and occurs specifically within vulnerable neurons in ALS/FTD.
Microstructural and isotopic analysis of shocked monazite from the Hiawatha impact structure: development of porosity and its utility in dating impact craters
Authors: Hyde William R. , Kenny Gavin G. , Whitehouse Martin J. , Wirth Richard , Roddatis Vladimir , Schreiber Anja , Garde Adam A. , Plan Anders , Larsen Nicolaj K. 
Published: March 2024

AbstractU–Pb geochronology of shocked monazite can be used to date hypervelocity impact events. Impact-induced recrystallisation and formation of mechanical twins in monazite have been shown to result in radiogenic Pb loss and thus constrain impact ages. However, little is known about the effect of porosity on the U–Pb system in shocked monazite. Here we investigate monazite in two impact melt rocks from the Hiawatha impact structure, Greenland by means of nano- and micrometre-scale techniques. Microstructural characterisation by scanning electron and transmission electron microscopy imaging and electron backscatter diffraction reveals shock recrystallisation, microtwins and the development of widespread micrometre- to nanometre-scale porosity. For the first time in shocked monazite, nanophases identified as cubic Pb, Pb3O4, and cerussite (PbCO3) were observed. We also find evidence for interaction with impact melt and fluids, with the formation of micrometre-scale melt-bearing channels, and the precipitation of the Pb-rich nanophases by dissolution–precipitation reactions involving pre-existing Pb-rich high-density clusters. To shed light on the response of monazite to shock metamorphism, high-spatial-resolution U–Pb dating by secondary ion mass spectrometry was completed. Recrystallised grains show the most advanced Pb loss, and together with porous grains yield concordia intercept ages within uncertainty of the previously established zircon U–Pb impact age attributed to the Hiawatha impact structure. Although porous grains alone yielded a less precise age, they are demonstrably useful in constraining impact ages. Observed relatively old apparent ages can be explained by significant retention of radiogenic lead in the form of widespread Pb nanophases. Lastly, we demonstrate that porous monazite is a valuable microtexture to search for when attempting to date poorly constrained impact structures, especially when shocked zircon or recrystallised monazite grains are not present.