bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure
Authors: Ries Benjamin , Normak Karl , Weiß R. Gregor , Rieder Salomé , Barros Emília P. , Champion Candide , König Gerhard , Riniker Sereina 
Published: January 2022

AbstractThe calculation of relative free-energy differences between different compounds plays an important role in drug design to identify potent binders for a given protein target. Most rigorous methods based on molecular dynamics simulations estimate the free-energy difference between pairs of ligands. Thus, the comparison of multiple ligands requires the construction of a “state graph”, in which the compounds are connected by alchemical transformations. The computational cost can be optimized by reducing the state graph to a minimal set of transformations. However, this may require individual adaptation of the sampling strategy if a transformation process does not converge in a given simulation time. In contrast, path-free methods like replica-exchange enveloping distribution sampling (RE-EDS) allow the sampling of multiple states within a single simulation without the pre-definition of alchemical transition paths. To optimize sampling and convergence, a set of RE-EDS parameters needs to be estimated in a pre-processing step. Here, we present an automated procedure for this step that determines all required parameters, improving the robustness and ease of use of the methodology. To illustrate the performance, the relative binding free energies are calculated for a series of checkpoint kinase 1 inhibitors containing challenging transformations in ring size, opening/closing, and extension, which reflect changes observed in scaffold hopping. The simulation of such transformations with RE-EDS can be conducted with conventional force fields and, in particular, without soft bond-stretching terms.
Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange
Authors: Markthaler Daniel , Kraus Hamzeh , Hansen Niels 
Published: January 2022

AbstractUmbrella sampling along a one-dimensional order parameter in combination with Hamiltonian replica exchange was employed to calculate the binding free energy of five guest molecules with known affinity to cucurbit[8]uril. A simple empirical approach correcting for the overestimation of the affinity by the GAFF force field was proposed and subsequently applied to the seven guest molecules of the “Drugs of Abuse” SAMPL8 challenge. Compared to the uncorrected binding free energies, the systematic error decreased but quantitative agreement with experiment was only reached for a few compounds. From a retrospective analysis a weak point of the correction term was identified.
Intrahousehold Bargaining Power in Spain: An Empirical Test of the Collective Model
Authors: Molina José Alberto , Velilla Jorge , Ibarra Helena 
Published: January 2022

AbstractThis paper analyzes the intrahousehold bargaining power of spouses in Spanish families, in a collective framework. We estimate household labor supply equations and, under certain testable restrictions, we obtain a theoretically derived sharing rule for household income, which characterizes intrahousehold bargaining power. Then, using unique data on decision-making in the household, we construct Pareto weights, and study the validity of the collective model by comparing the theoretical sharing rule and the constructed Pareto weight. The results reveal that both the observed Pareto weight and the theoretical sharing rule display qualitative similarities, thus providing direct empirical support to the collective model. Furthermore, the results suggest that Spanish wives behave more altruistically, while husbands behave more egoistically. This should be taken into account by policy makers and researchers when analyzing inequality in the household, and contemplating specific policies affecting the household.
Comparison of algorithms for error prediction in manufacturing with automl and a cost-based metric
Authors: Gerling Alexander , Ziekow Holger , Hess Andreas , Schreier Ulf , Seiffer Christian , Abdeslam Djaffar Ould 
Published: January 2022

AbstractIn order to manufacture products at low cost, machine learning (ML) is increasingly used in production, especially in high wage countries. Therefore, we introduce our PREFERML AutoML system, which is adapted to the production environment. The system is designed to predict production errors and to help identifying the root cause. It is particularly important to produce results for further investigations that can also be used by quality engineers. Quality engineers are not data science experts and are usually overwhelmed with the settings of an algorithm. Because of this, our system takes over this task and delivers a fully optimized ML model as a result. In this paper, we give a brief overview of what results can be achieved with a state-of-the-art classifier. Moreover, we present the results with optimized tree-based algorithms based on RandomSearchCV and HyperOpt hyperparameter tuning. The algorithms are optimized based on multiple metrics, which we will introduce in the following sections. Based on a cost-oriented metric we can show an improvement for companies to predict the outcome of later product tests. Further, we compare the results from the mentioned optimization approaches and evaluate the needed time for them.
Tunable magnetocaloric effect in amorphous Gd-Fe-Co-Al-Si alloys
Authors: Lindner Natalia , Śniadecki Zbigniew , Kołodziej Mieszko , Grenèche Jean-Marc , Marcin Jozef , Škorvánek Ivan , Idzikowski Bogdan 
Published: January 2022

AbstractA magnetocaloric effect with wide tunability was observed in melt-spun amorphous Gd65Fe15-xCo5+xAl10Si5 (x = 0, 5, 10) alloys of different Fe/Co ratios. Their magnetic properties were compared with those of the previously investigated parent alloy Gd65Fe10Co10Al15. The glassy structure of the melt-spun samples was confirmed by X-ray diffraction (XRD) and 57Fe Mössbauer spectrometry. Their Curie temperatures (TC) were between 155 and 195 K and increased significantly with decreasing Co content. The highest value of the magnetic entropy change ΔSM = − 6.8 J/kg K was obtained for Gd65Fe5Co15Al10Si5, when the magnetic field was increased from 0 to 5 T. Refrigerant capacity (RC) takes values close to 700 J/kg for the whole series of the alloys. The occurrence of the second-order phase transition and the conformity of the magnetic behavior with the mean field model were concluded on the basis of the analysis of the universal curves and the values of the exponent n (ΔSM ∝ Hn).
Graphical abstract
In situ polymerization monitoring of a diacrylate in an electrically conducting mesoporous nanoparticle scaffold
Authors: Hoffmann Ron , Naatz Hendrik , Hartwig Andreas 
Published: January 2022

AbstractThe properties of nanoparticle–polymer composites strongly depend on the network structure of the polymer matrix. By introducing nanoparticles into a monomer (solution) and subsequently polymerizing it, the formation of the polymer phase influences the mechanical and physicochemical properties of the composite. In this study, semi-conducting indium tin oxide (ITO) nanoparticles were prepared to form a rigid nanoparticle scaffold in which 1,6-hexanediol diacrylate (HDDA), together with an initiator for photo-polymerization, was infiltrated and subsequently polymerized by UV light. During this process, the polymerization reaction was characterized using rapid scan Kubelka–Munk FT-IR spectroscopy and compared to bulk HDDA. The conductivity change of the ITO nanoparticles was monitored and correlated with the polymerization process. It was revealed that the reaction rates of the radical initiation and chain propagation are reduced when cured inside the voids of the nanoparticle scaffold. The degree of conversion is lower for HDDA infiltrated into the mesoporous ITO nanoparticle scaffold compared to purely bulk-polymerized HDDA.
Graphical abstract
PEEK filament characteristics before and after extrusion within fused filament fabrication process
Authors: Comelli Cleiton André , Davies Richard , van der Pol HenkJan , Ghita Oana 
Published: January 2022

AbstractThe heating and extrusion process in fused filament fabrication (FFF) is significantly shorter than the conventional extrusion process where longer heating times and significant pressure are applied. For this reason, it is important to understand whether the crystal history of the feedstock is fully erased through the FFF process and whether the FFF process can be tailored further by engineering the crystallization of the feedstock filaments. In this context, a methodology for evaluating the influence of morphology and mechanical properties on different feedstock and extruded filaments is proposed. Filaments with three different PEEK 450G crystalline structures (standard crystallinity, drawn filament and amorphous filament) were selected and evaluated, before and after free extrusion. The resulting morphology, crystallinity and mechanical properties of the extruded filaments were compared against the feedstock properties. X-ray diffraction (XRD), transmission electron microscopy (TEM), differential and fast scanning calorimetry (DSC/FDSC) and tensile test were the techniques used to evaluate the materials. The results showed clear differences in the properties of the feedstock materials, while the analysis of the extruded filaments points to a homogenization of the resulting material producing mostly similar mechanical properties. However, the use of the drawn filament highlighted a statistically significant improvement in crystallinity and mechanical performance, especially in strain values. This conclusion suggests the innovative possibility of improving the quality of manufactured parts by tailoring the microstructure of the feedstock material used in the FFF process.
Graphical abstract
A viewpoint on material and design considerations for oesophageal stents with extended lifetime
Authors: Jackson Caitlin E. , Johnson Liam S. J. , Williams Dominic A. , Laasch Hans-Ulrich , Edwards Derek W. , Harvey Alison G. 
Published: January 2022

AbstractOesophageal stents are meshed tubular implants designed to maintain patency of the oesophageal lumen and attenuate the symptoms of oesophageal cancer. Oesophageal cancers account for one in twenty cancer diagnoses and can lead to dysphasia, malnutrition and the diminishment of patient quality of life (QOL). Self-expanding oesophageal stents are the most common approach to attenuate these symptoms. Recent advances in oncological therapy have enabled patient survival beyond the lifetime of current devices. This introduces new complications for palliation, driving the need for innovation in stent design. This review identifies the factors responsible for stent failure. It explores the challenges of enhancing the longevity of stent therapies and outlines solutions to improving clinical outcomes. Discussions focus on the role of stent materials, construction methods, and coatings upon device performance. We found three key stent enhancement strategies currently used; material surface treatments, anti-migratory modifications, and biodegradable skeletons. Furthermore, radioactive and drug eluting stent designs were identified as emerging novel treatments. In conclusion, the review offers an overview of remaining key challenges in oesophageal stent design and potential solutions. It is clear that further research is needed to improve the clinical outcome of stents and patient QOL.
Conductivity, microstructure and mechanical properties of tape-cast LATP with LiF and SiO2 additives
Authors: Gross Jürgen Peter , Malzbender Jürgen , Dashjav Enkhtsetseg , Tietz Frank , Schwaiger Ruth 
Published: January 2022

AbstractLATP sheets with LiF and SiO2 addition prepared by tape cast as electrolytes for solid-state batteries were characterized regarding conductivity, microstructure and mechanical properties aiming toward an optimized composition. The use of additives permitted a reduction of the sintering temperature. Rietveld analyses of the samples with additives revealed a phase mixture of NaSICON modifications crystallizing with rhombohedral and orthorhombic symmetry as a superstructure with space group Pbca. It seems that LiF acts as a sintering additive but also as a mineralizer for the superstructure of LATP. As general trend, higher LiF to SiO2 ratios led to lower porosities and higher values of elastic modulus and hardness determined by indentation testing, but the presence of the orthorhombic LATP leads to a decrease in the ionic conductivity. Micro-pillar testing was used to assess the crack growth behavior revealing weak grain boundaries.
A study of tensile and bending properties of 3D-printed biocompatible materials used in dental appliances
Authors: García Reyes Marcos , Bataller Torras Alex , Cabrera Carrillo Juan A. , Velasco García Juan M. , Castillo Aguilar Juan J. 
Published: January 2022

AbstractIn the last years, a large number of new biocompatible materials for 3D printers have emerged. Due to their recent appearance and rapid growth, there is little information about their mechanical properties. The design and manufacturing of oral appliances made with 3D printing technologies require knowledge of the mechanical properties of the biocompatible material used to achieve optimal performance for each application. This paper focuses on analysing the mechanical behaviour of a wide range of biocompatible materials using different additive manufacturing technologies. To this end, tensile and bending tests on different types of recent biocompatible materials used with 3D printers were conducted to evaluate the influence of the material, 3D printing technology, and printing orientation on the fragile/ductile behaviour of the manufactured devices. A test bench was used to perform tensile tests according to ASTM D638 and bending tests according to ISO 178. The specimens were manufactured with nine different materials and five manufacturing technologies. Furthermore, specimens were created with different printing technologies, biocompatible materials, and printing orientations. The maximum allowable stress, rupture stress, flexural modulus, and deformation in each of the tested specimens were recorded. Results suggest that specimens manufactured with Stereolithography (SLA) and milling (polymethyl methacrylate PMMA) achieved high maximum allowable and rupture stress values. It was also observed that Polyjet printing and Selective Laser Sintering technologies led to load–displacement curves with low maximum stress and high deformation values. Specimens manufactured with Digital Light Processing technology showed intermediate and homogeneous performance. Finally, it was observed that the printing direction significantly influences the mechanical properties of the manufactured specimens in some cases.
Global optimization for the multilevel European gas market system with nonlinear flow models on trees
Authors: Schewe Lars , Schmidt Martin , Thürauf Johannes 
Published: January 2022

AbstractThe European gas market is implemented as an entry-exit system, which aims to decouple transport and trading of gas. It has been modeled in the literature as a multilevel problem, which contains a nonlinear flow model of gas physics. Besides the multilevel structure and the nonlinear flow model, the computation of so-called technical capacities is another major challenge. These lead to nonlinear adjustable robust constraints that are computationally intractable in general. We provide techniques to equivalently reformulate these nonlinear adjustable constraints as finitely many convex constraints including integer variables in the case that the underlying network is tree-shaped. We further derive additional combinatorial constraints that significantly speed up the solution process. Using our results, we can recast the multilevel model as a single-level nonconvex mixed-integer nonlinear problem, which we then solve on a real-world network, namely the Greek gas network, to global optimality. Overall, this is the first time that the considered multilevel entry-exit system can be solved for a real-world sized network and a nonlinear flow model.
The robust bilevel continuous knapsack problem with uncertain coefficients in the follower’s objective
Authors: Buchheim Christoph , Henke Dorothee 
Published: January 2022

AbstractWe consider a bilevel continuous knapsack problem where the leader controls the capacity of the knapsack and the follower chooses an optimal packing according to his own profits, which may differ from those of the leader. To this bilevel problem, we add uncertainty in a natural way, assuming that the leader does not have full knowledge about the follower’s problem. More precisely, adopting the robust optimization approach and assuming that the follower’s profits belong to a given uncertainty set, our aim is to compute a solution that optimizes the worst-case follower’s reaction from the leader’s perspective. By investigating the complexity of this problem with respect to different types of uncertainty sets, we make first steps towards better understanding the combination of bilevel optimization and robust combinatorial optimization. We show that the problem can be solved in polynomial time for both discrete and interval uncertainty, but that the same problem becomes NP-hard when each coefficient can independently assume only a finite number of values. In particular, this demonstrates that replacing uncertainty sets by their convex hulls may change the problem significantly, in contrast to the situation in classical single-level robust optimization. For general polytopal uncertainty, the problem again turns out to be NP-hard, and the same is true for ellipsoidal uncertainty even in the uncorrelated case. All presented hardness results already apply to the evaluation of the leader’s objective function.
Optimistic NAUTILUS navigator for multiobjective optimization with costly function evaluations
Authors: Saini Bhupinder Singh , Emmerich Michael , Mazumdar Atanu , Afsar Bekir , Shavazipour Babooshka , Miettinen Kaisa 
Published: January 2022

AbstractWe introduce novel concepts to solve multiobjective optimization problems involving (computationally) expensive function evaluations and propose a new interactive method called O-NAUTILUS. It combines ideas of trade-off free search and navigation (where a decision maker sees changes in objective function values in real time) and extends the NAUTILUS Navigator method to surrogate-assisted optimization. Importantly, it utilizes uncertainty quantification from surrogate models like Kriging or properties like Lipschitz continuity to approximate a so-called optimistic Pareto optimal set. This enables the decision maker to search in unexplored parts of the Pareto optimal set and requires a small amount of expensive function evaluations. We share the implementation of O-NAUTILUS as open source code. Thanks to its graphical user interface, a decision maker can see in real time how the preferences provided affect the direction of the search. We demonstrate the potential and benefits of O-NAUTILUS with a problem related to the design of vehicles.
Exploratory Considerations in Chemistry Education—Didactic Modelling for Complexity in Students’ Discussions
Authors: Dudas Cecilia , Rundgren Carl-Johan , Lundegård Iann 
Published: January 2022

AbstractResearch has shown the importance of dealing with real-life issues and of enabling student encounters with complexity in chemistry education in order to increase student participation. Therefore, this study aims to analyse how complexity evolves in students’ discussions and how this complexity relates to aspects of tentativeness in chemistry. In the study, we analyse how a previously developed didactic model can be refined from the students’ considerations evolving from the present context. The study was conducted as an in situ study in one upper-secondary school. Students’ discussions were recorded on video. The recordings were transcribed and analysed using deliberative educational questions. Two different kinds of considerations emerged in the students’ discussions: factual and exploratory considerations. While factual considerations are an important element of chemistry education, students also need to encounter exploratory considerations. The study proposes a didactic model useful for teachers in didactic analysis and design of activities aiming to support students to unfold complexity through exploratory considerations. One implication is to base activities on real-life issues in order to invite the unpredictability needed for experiencing complexity and the exploratory nature of chemistry. These issues enable students to experience aspects of tentativeness in chemistry and thereby increase their understanding of NOS and chemistry as a knowledge building practice. Furthermore, this might also increase student participation in chemistry education.
Purinergic receptors mediate endothelial dysfunction and participate in atherosclerosis
Authors: Wu Xian-Ming , Zhang Ning , Li Jiang-Shan , Yang Zhi-Hong , Huang Xiao-Lou , Yang Xiao-Fang 
Published: January 2022

Abstract
Atherosclerosis is the main pathological basis of cardiovascular disease and involves damage to vascular endothelial cells (ECs) that results in endothelial dysfunction (ED). The vascular endothelium is the key to maintaining blood vessel health and homeostasis. ED is a complex pathological process involving inflammation, shear stress, vascular tone, adhesion of leukocytes to ECs, and platelet aggregation. The activation of P2X4, P2X7, and P2Y2 receptors regulates vascular tone in response to shear stress, while activation of the A2A, P2X4, P2X7, P2Y1, P2Y2, P2Y6, and P2Y12 receptors promotes the secretion of inflammatory cytokines. Finally, P2X1, P2Y1, and P2Y12 receptor activation regulates platelet activity. These purinergic receptors mediate ED and participate in atherosclerosis. In short, P2X4, P2X7, P2Y1, and P2Y12 receptors are potential therapeutic targets for atherosclerosis.
The Comparison of the Dietary Intake Loss Between Elderly and Non-Elderly Patients After Gastrectomy for Gastric Cancer
Authors: Nakazono Masato , Aoyama Toru , Komori Keisuke , Watanabe Hayato , Kano Kazuki , Nagasawa Shinsuke , Segami Kenki , Tamagawa Hiroshi , Yukawa Norio , Rino Yasushi , Ogata Takashi , Oshima Takashi 
Published: January 2022

Abstract
Background/Aim
The present study quantified the changes in the dietary and nutritional intake after gastrectomy between elderly and non-elderly patients.

Patients and Methods
This prospective observational study enrolled patients who underwent curative gastrectomy for gastric cancer.

Results
Twenty-three patients ≥ 75 years old were classified into the elderly group, and 127 patients < 75 years old were classified into the non-elderly group. The respective median % dietary intake losses at 1 and 3 months postoperatively were −12.4% and −5.3% in the elderly group and −8.3% and −2.8% in the non-elderly group (p = 0.075 and 0.080). On comparing the intake loss of three major nutrients, the respective median % lipid intake losses at 1 and 3 months postoperatively were −13.5% and −5.8% in the elderly group and −7.3% and 0% in the non-elderly group (p = 0.029 and 0.045).

Conclusion
Our results suggested that elderly patients experienced more serious lipid intake loss after gastrectomy than non-elderly patients.