bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of dendritic grain structures with a Cellular Automaton – Parabolic Thick Needle model
Authors: Wu Y , Senninger O , Gandin Ch-A 
Published: March 2023

Abstract
A multiscale numerical model, coupling the Cellular Automaton (CA) method to the Parabolic Thick Needle (PTN) method, is developed to compute dendritic microstructures. It is applied to directional solidification of bi-crystals under a frozen temperature approximation with fixed temperature gradient and fixed cooling rate. A dendritic branch is modeled as a cylinder headed by a parabolic tip. Its kinetics is computed using the PTN method from the composition field in the liquid in the vicinity of the parabola. This dendritic branch takes part in the definition of a grain envelope by its integration in a CA growth algorithm. The so-called Cellular Automaton – Parabolic Thick Needle (CAPTN) model can simulate the growth of dendritic grains while accounting for non-steady diffusion fields. The PTN method is implemented using Finite Element (FE) method on a heterogeneous mesh. An adaptive FE mesh strategy is developed to optimize computational time. The grain boundary orientation angle of a diverging bi-crystal configuration is investigated at steady state and compared to the Phase-Field (PF) method and the classical CA method. It is shown that contrary to the CA method, the CAPTN model is in good agreement with data deduced from PF simulations, demonstrating the interest of this coupling in the modeling of dendritic growth.
Time evolution of interface shape distribution of equiaxed dendrite: A phase-field study
Authors: Ohno Munekazu , Kudo Mikihiro , Kim Geunwoo , Yamada Ryo , Shibuta Yasushi , Takaki Tomohiro 
Published: March 2023

Abstract
An understanding of the morphology of growing dendrites in alloys is needed for an analysis of microsegregation, as well as an estimation of the permeability for macroscopic fluid dynamics. Quantitative phase-field simulations were used to study the growth process of three-dimensional (3D) equiaxed dendrites in an Al-1.0 mass%Cu alloy during continuous cooling. The dendrites were analysed using an interface shape distribution (ISD) map, which provides the probability of the local interface having a morphology with a given curvedness (C) and shape factor (S). Morphological changes in the microstructure can be measured sensitively from the change in the average value of the curvedness 〈C〉 relative to the solid volume fraction. The ISD map continued to change over time during continuous cooling, implying that it was not time-invariant. Furthermore, when microstructural changes occurred, similarities between the ISD maps were observed, independent of the cooling rates and system sizes.
Phase-field lattice Boltzmann model of growth and buoyancy driven motion of dendritic particles: the effect of Coriolis force
Authors: Rátkai L , Gránásy L , Pusztai T 
Published: March 2023

Abstract
A phase-field lattice Boltzmann (PFLB) model we developed recently (Rátkai L, Pusztai T and Gránásy L 2019 npj Comput. Mater.
5 113) was adapted to investigate the effect of Coriolis force on the solidification morphology forming in a centrifuge. The moving particles are handled using an overlapping multi-grid scheme, assigning a separate moving grid to each individual particle, with attached local fields. Relying on this approach, solidification problems, in which solute diffusion, melt flow, solid motion, the effect of gravity and collision of the particles occur simultaneously can be modelled. Using relevant properties of an Al-Ti alloy, the interaction of columnar and equiaxed solidification was studied. It was found that the Coriolis force influences the path of the falling dendritic particles, which in turn governs the position, at which the transition between columnar and equiaxed morphologies takes place.
Characterisation of mesosegregations in large steel ingots
Authors: Gutman L , Kennedy J R , Roch F , Clément A Marceaux dit , Salsi L , Cauzid J , Rouat B , Combeau H , Založnik M , Zollinger J 
Published: March 2023

Abstract
The chemical composition mapping of low-alloyed steel ingots used for the nuclear industry is crucial in the manufacturing of forgings and their final quality mastering. Mechanical properties of forged and hot-rolled steels may be affected by chemically segregated bands. These bands arise from segregations that appear at the scale of a few grains in the as-cast structure: the so-called mesosegregations. While segregation at the scale of dendrite arms (microsegregation) and the scale of the casting (macrosegregation) is well understood and can be readily characterized, only little is known about the formation of mesosegregation. The first step towards understanding the cause behind mesosegregation formation can be brought through comprehensive chemical characterisation at the scale of several grains (mesoscopic scale), which requires using different characterisation techniques compared to micro- or macrosegregation characterisation. We developed a sampling and characterisation methodology that allows segregations to be mapped at the mesoscopic scale using micro X-ray fluorescence (μXRF). Characterisation technique, sampling methodology, and sample size must be adapted to consider the different solidification structures; both at smaller (dendrite arms, grains) and larger (macrostructure) scales. Segregations were characterised on a 113 x 98 mm2 steel plate extracted from a low-alloyed steel large ingot.
Computational fluid dynamics calculations of binary representation of Ni-base superalloy solidification in frustum geometries
Authors: Allen J D T , Green N , Warnken N 
Published: March 2023

Abstract
CFD calculations were carried out on a number of frustum geometries from the experimental literature on freckling of superalloys. The effects of two imposed thermal fields were investigated, flat and inclined. Experiments document that when thermal fields are inclined the cold side is more prone to formation of freckles; our results conclude that rising liquid plumes in advance of the solidification front, which can correlate to freckles, are more abundant and intense on the cold side. Also, modelled plume activity is greater in inward sloping frustum geometries as opposed to outward sloping ones, which also agrees with established literature. Complex flow patterns were observed in inclined geometries and there is a clear interplay and competition between both the thermal and solutal aspects of flow, with flow being significantly changed, sometimes reversed in direction in some capacity. Our results also offer insight into the incubation length for plume and resultant freckle formation after the transition between frustums, with some critical distance of advance of the solidification front necessary to initiate and establish other plumes that feed into the main one circulating liquid flow which is locally intense enough to potentially create a freckle.
Growth of Si particles and Al dendrites during solidification of a hypereutectic Al-Si-Cu alloy
Authors: Zimmermann G , Sturz L , Schaberger-Zimmermann E , Pickmann Ch 
Published: March 2023

Abstract
Hypereutectic Al-Si alloys containing up to 16-20 wt% Si and often several wt% Cu are widely applied in automobile and aerospace industry, because of their high wear resistance and high-temperature resistance. The mechanical and physical properties of these alloys are strongly influenced by the size and morphology of the primary silicon particles. Here, rod-like bulk samples of hypereutectic Al-18wt%Si-10wt%Cu alloys were solidified in a Bridgman-Stockbarger furnace with different solidification parameters. Microstructure analysis of longitudinal and radial cross-sections demonstrated nearly equiaxed growth of Silicon particles in the 3D samples. At low cooling rate a few but larger Si particles exist compared to many and smaller Si particles for solidification with higher cooling rate. Also the structure of the Al dendrites is much finer at higher cooling rates. Additionally, sheet-like samples were solidified under isothermal cooling conditions. A real-time observation method using X-ray radiography allowed for the in-situ observation. During cooling down below the liquidus temperature, facetted Si particles are the first to nucleate. Reaching the nucleation temperature of Al, growth of non-facetted Al dendrites was observed simultaneously in the whole melt, generally not starting from the surface of existing Si particles. Some Al dendrites growing in the plane of the sheet-like samples develop rather rapidly in one direction, whereas other Al dendrites grow more equiaxed, which is attributed to different grain orientations of the Al-rich dendrites in quasi-2D solidification.
Solidification of Al-Mn-based alloys under various processing parameters
Authors: Markoli B , Leskovar B , Zaky A , Naglič I 
Published: March 2023

Abstract
A number of Al-Mn-based alloys were investigated with a view to their commercialization. Various casting techniques were used to affect the constitution of the alloys studied from crystalline to quasi-crystalline as well as other metastable states. Variations in cooling rates and chemical composition, along with other processing parameters, have been shown to allow us to control the final constitution and properties of what we believe could be the next generation of commercial Al-based alloys.
Our research has shown that the solidification process of Al-Mn based alloys with additions of other metallic elements can lead to the formation of very complex final states, opening up possibilities for designing and controlling the properties of alloys.
The solidification process in the alloys studied proved to be very complex, but can be explained by basic knowledge of the crystallisation of metallic melts. We have discovered that by changing the processing parameters and the chemical composition of the alloys in a controlled way, it is possible to tailor the final properties of the alloys, making them attractive for commercial purposes.
Microphysiological systems to study colorectal cancer: state-of-the-art
Authors: Ramos Pedro , Carvalho Mariana R , Chen Wei , Yan Le-Ping , Zhang Chang-Hua , He Yu-long , Reis Rui L , Oliveira Joaquim M 
Published: March 2023

Abstract
Basic pre-clinical research based on 2D cultures have been very valuable in colorectal cancer (CRC) research but still have failed to improve patient prognostic outcomes. This is because they simply do not replicate what happens in vivo, i.e. 2D cultured cells system cannot replicate the diffusion constraints usually found in the body. Importantly, they also do not mimic the dimensionality of the human body and of a CRC tumour (3D). Moreover, 2D cultures lack the cellular heterogeneity and the tumour microenvironment (TME) such as stromal components, blood vessels, fibroblasts, and cells of the immune system. Cells behave differently whether in 2D and 3D, in particular their different genetic and protein expression panels are very different and therefore we cannot fully rely on drug tests done in 2D. A growing field of research based on microphysiological systems involving organoids/spheroids or patient-derived tumour cells has become a solid base for a better understanding of the TME and as a result is a step towards personalized medicine. Furthermore, microfluidic approaches have also started to open possibilities of research, with tumour-on-chips and body-on-chips being used in order to decipher complex inter-organ signalling and the prevalence of metastasis, as well as CRC early-diagnosis through liquid biopsies. Herein, we focus on the state-of-the-art of CRC research with emphasis on 3D microfluidic in vitro cultures—organoids, spheroids—drug resistance, circulating tumour cells and microbiome-on-a-chip technology.
Experimental and finite element simulation study of the mechanical behaviors of aluminum foam-filled single/double tubes
Authors: Yanjun Zhao , Yunfei Cao , Liuyang Li , Jingrui Zhang , Xiukang Chen 
Published: March 2023

Abstract
Aluminum foam-filled tubes are complicated structures created by filling one or more thin-walled metal tubes with varying shapes in cross-sections with aluminum foam. We optimized the structure of aluminum foam-filled tubes using software simulation, compression, and three-point bending experiments. Filling aluminum foam not only improves the axial compressive performance and bending strength of the thin-walled metal tube but also eliminates the disadvantage of the low strength of the aluminum foam. The aluminum foam-filled single tube exhibited significant improvements in load-bearing and energy absorption, with a one-time increase in load-bearing and five times increase in energy absorption compared with an empty tube. The aluminum foam-filled single tube with a smaller diameter-to-thickness ratio has a higher load-bearing capacity. In contrast, the length-to-diameter ratio has a lower impact on load-bearing capacity. Once the filling length reaches the effective filling length, the structure can still support higher loads and effectively reduce its overall weight. The compression and bending properties in the double-tube structure filled with foam aluminum improved significantly compared with the empty tube and single-tube structure filled with aluminum foam. The total compressive energy absorption capacity in the double-tube structure filled with aluminum foam is 2.01 times that of the empty tube and 1.81 times that in the single-tube-filled structure. When the wall thickness of the filled stainless steel tube is 1.0 mm, the total bending energy absorption and the specific absorption energy of the aluminum foam-filled double tube structure are 1.5 and 2.1 times that of the corresponding aluminum foam-filled single tube, respectively.
Disentangling the effect of the hole-transporting layer, the bottom, and the top device on the fill factor in monolithic CIGSe-perovskite tandem solar cells by using spectroscopic and imaging tools
Authors: Kafedjiska I , Farias Basulto G , Ruske F , Maticiuc N , Bertram T , Kaufmann C A , Schlatmann R , Lauermann I 
Published: March 2023

Abstract
We present monolithic copper–indium–gallium–diselenide (Cu(In,Ga)Se2, CIGSe)-perovskite tandem solar cells with air- or N2-transferred NiO
x
:Cu with or without self-assembled monolayer (SAM) as a hole-transporting layer (HTL). A champion efficiency of 23.2%, open-circuit voltage (V

o
c

) of 1.69 V, and a fill factor (FF) of 78.3% are achieved for the tandem with N2-transferred NiO
x
:Cu + SAM. The samples with air-transferred NiO
x
:Cu + SAM have V

o
c

and FF losses, while those without SAM are heavily shunted. We find via x-ray and UV photoelectron spectroscopy that the air exposure leads to non-negligible loss in the Ni2+ species and changes in the NiO
x
:Cu’s work function and valence band maxima, both of which can negatively impact the V

o
c

and the FF of the tandems. Furthermore, by performing dark lock-in thermography, photoluminescence (PL), and scanning electron microscopy studies, we are able to detect various morphological defects in the tandems with poor performance, such as ohmic shunts originating from defects in the bottom CIGSe cell, or from cracking/delaminating of the perovskite top cell. Finally, by correlating the detected shunts in the tandems with PL-probed bottom device, we can conclude that not all defects in the bottom device induce ohmic shunts in the tandems since the NiO
x
:Cu + SAM HTL bi-layer can decouple the growth of the top device from the rough, defect-rich and defect-tolerant bottom device and enable high-performing devices.
Skin effect suppression for millimeter-wave frequencies through manipulation of permeability
Authors: Yamada Hidenori 
Published: March 2023

Abstract
A new device strategy for suppressing unwanted skin effect in coplanar transmission lines at frequencies beyond 20 GHz is presented. Utilization of the anti-resonance point as a source of imaginary permeability to suppress the skin effect is proposed. This idea is backed up by Kramers-Kronig and published experiments. The principle is independent of Landau–Lifshitz-Gilbert magnetic precession damping. The present work contributes both a greater understanding of skin effect manipulation and a method for obtaining zero skin effect using known laminate materials.
Histologic and Clinical Outcomes of Patients Developing Post–Liver Transplant Plasma Cell–Rich Rejection
Authors: Ozturk Nazli Begum , Schiano Thomas D , Fiel Maria Isabel 
Published: March 2023

Abstract

Objectives
Plasma cell–rich rejection (PCCR), also known as “plasma cell hepatitis” or “de novo autoimmune hepatitis,” is a cause of allograft dysfunction occurring post–liver transplantation (LT). Patients often develop allograft failure and may require repeat LT. PCRR may fall within the spectrum of different histologies associated with antibody-mediated rejection (AMR), which is associated with donor-specific antibodies (DSAs) and positive complement component C4 (C4d) immunostaining. We sought to analyze the histologic and clinical outcomes of patients having biopsy-proven PCRR as well as to examine its C4d staining and DSA profiles.

Methods
We identified patients having PCRR between 2000 and 2020 using the electronic pathology database at our institution. We included patients who underwent at least one follow-up liver biopsy after establishing the PCRR diagnosis to assess future histologic progression and outcomes. Mean fluorescence intensity for at least one single DSA of 2,000 or higher was considered positive. Histologic diagnosis of PCRR was independently made by an experienced liver pathologist.

Results
A total of 35 patients were included in the study. Hepatitis C virus was the most common etiology for LT (59.5%). Mean ± SD age at LT was 49.0 ± 12.7 years. Forty percent of patients developed PCRR within 2 years of LT. Most patients (68.5%) had negative outcomes, with progression from PCRR to cirrhosis or chronic ductopenic rejection (CDR). Patients who had hepatitis C virus were more likely to develop cirrhosis rather than CDR following the PCRR diagnosis (P = .01). Twenty-three (65.7%) patients had at least one prior episode of T-cell–mediated rejection before being diagnosed with PCRR. DSAs were positive in 16 of 19 patients assessed, and C4d immunostaining was positive in 9 of 10 patients.

Conclusions
Development of PCRR negatively affects liver allograft outcomes and patient survival after LT. The presence of DSA and C4d in PCRR patients supports it to be within the histologic spectrum of AMR.
WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity
Authors: Liu Baqiao , Warnow Tandy 
Published: March 2023

AbstractSummaryMultiple sequence alignment is a basic part of many bioinformatics pipelines, including in phylogeny estimation, prediction of structure for both RNAs and proteins, and metagenomic sequence analysis. Yet many sequence datasets exhibit substantial sequence length heterogeneity, both because of large insertions and deletions in the evolutionary history of the sequences and the inclusion of unassembled reads or incompletely assembled sequences in the input. A few methods have been developed that can be highly accurate in aligning datasets with sequence length heterogeneity, with UPP one of the first methods to achieve good accuracy, and WITCH a recent improvement on UPP for accuracy. In this article, we show how we can speed up WITCH. Our improvement includes replacing a critical step in WITCH (currently performed using a heuristic search) by a polynomial time exact algorithm using Smith–Waterman. Our new method, WITCH-NG (i.e. ‘next generation WITCH’) achieves the same accuracy but is substantially faster. WITCH-NG is available at https://github.com/RuneBlaze/WITCH-NG.Availability and implementationThe datasets used in this study are from prior publications and are freely available in public repositories, as indicated in the Supplementary Materials.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction
Authors: Wu Zhourun , Guo Mingyue , Jin Xiaopeng , Chen Junjie , Liu Bin 
Published: March 2023

AbstractMotivationProtein function annotation is fundamental to understanding biological mechanisms. The abundant genome-scale protein–protein interaction (PPI) networks, together with other protein biological attributes, provide rich information for annotating protein functions. As PPI networks and biological attributes describe protein functions from different perspectives, it is highly challenging to cross-fuse them for protein function prediction. Recently, several methods combine the PPI networks and protein attributes via the graph neural networks (GNNs). However, GNNs may inherit or even magnify the bias caused by noisy edges in PPI networks. Besides, GNNs with stacking of many layers may cause the over-smoothing problem of node representations.ResultsWe develop a novel protein function prediction method, CFAGO, to integrate single-species PPI networks and protein biological attributes via a multi-head attention mechanism. CFAGO is first pre-trained with an encoder–decoder architecture to capture the universal protein representation of the two sources. It is then fine-tuned to learn more effective protein representations for protein function prediction. Benchmark experiments on human and mouse datasets show CFAGO outperforms state-of-the-art single-species network-based methods by at least 7.59%, 6.90%, 11.68% in terms of m-AUPR, M-AUPR, and Fmax, respectively, demonstrating cross-fusion by multi-head attention mechanism can greatly improve the protein function prediction. We further evaluate the quality of captured protein representations in terms of Davies Bouldin Score, whose results show that cross-fused protein representations by multi-head attention mechanism are at least 2.7% better than that of original and concatenated representations. We believe CFAGO is an effective tool for protein function prediction.Availability and implementationThe source code of CFAGO and experiments data are available at: http://bliulab.net/CFAGO/.