bluuebunny/crossref_metadata_2025_split huggingface dataset:
Airfoil optimization using Design-by-Morphing
Authors: Sheikh Haris Moazam , Lee Sangjoon , Wang Jinge , Marcus Philip S 
Published: June 2023

Abstract
Design-by-Morphing (DbM) is a novel design methodology that creates a search space for topology optimization. Traditional design techniques often impose geometric constraints and, sometimes, the designer’s biases on the design space, which restricts the novelty of the designs and allows for only small local changes. On the contrary, we show in this paper that DbM does not impose such restrictions on the design space, thus allowing for a radical and expansive search space with only a few design parameters. We compare DbM with other methods in the case of design space generation for 2D airfoils and find that DbM can reconstruct the entire UIUC database with &gt;99.5% accuracy. Furthermore, using a bi-objective genetic algorithm, we optimize the airfoil designs created by DbM to maximize both the lift-over-drag ratio, CLDmax, and stall angle tolerance, Δα, which results in a Pareto-front of innovative airfoils that exhibit substantial improvements in both objectives.
Split liability assessment in car accident using 3D convolutional neural network
Authors: Lee Sungjae , Lee Yong-Gu 
Published: June 2023

Abstract
In a car accident, negligence is evaluated through a process known as split liability assessment. This assessment involves reconstructing the accident scenario based on information gathered from sources such as dashcam footage. The final determination of negligence is made by simulating the information contained in the video. Therefore, accident cases for split liability assessment should be classified based on information affecting the negligence degree. While deep learning has recently been in the spotlight for video recognition using short video clips, no research has been conducted to extract meaningful information from long videos, which are necessary for split liability assessment. To address this issue, we propose a new task for analysing long videos by stacking the important information predicted through the 3D CNNs model. We demonstrate the feasibility of our approach by proposing a split liability assessment method using dashcam footage.
Circulating proteome for pulmonary nodule malignancy
Authors: Khodayari Moez Elham , Warkentin Matthew T , Brhane Yonathan , Lam Stephen , Field John K , Liu Geoffrey , Zulueta Javier J , Valencia Karmele , Mesa-Guzman Miguel , Nialet Andrea Pasquier , Atkar-Khattra Sukhinder , Davies Michael P A , Grant Benjamin , Murison Kiera , Montuenga Luis M , Amos Christopher I , Robbins Hilary A , Johansson Mattias , Hung Rayjean J 
Published: June 2023

Abstract

Background
Although lung cancer screening with low-dose computed tomography is rolling out in many areas of the world, differentiating indeterminate pulmonary nodules remains a major challenge. We conducted one of the first systematic investigations of circulating protein markers to differentiate malignant from benign screen-detected pulmonary nodules.

Methods
Based on 4 international low-dose computed tomography screening studies, we assayed 1078 protein markers using prediagnostic blood samples from 1253 participants based on a nested case-control design. Protein markers were measured using proximity extension assays, and data were analyzed using multivariable logistic regression, random forest, and penalized regressions. Protein burden scores (PBSs) for overall nodule malignancy and imminent tumors were estimated.

Results
We identified 36 potentially informative circulating protein markers differentiating malignant from benign nodules, representing a tightly connected biological network. Ten markers were found to be particularly relevant for imminent lung cancer diagnoses within 1 year. Increases in PBSs for overall nodule malignancy and imminent tumors by 1 standard deviation were associated with odds ratios of 2.29 (95% confidence interval: 1.95 to 2.72) and 2.81 (95% confidence interval: 2.27 to 3.54) for nodule malignancy overall and within 1 year of diagnosis, respectively. Both PBSs for overall nodule malignancy and for imminent tumors were substantially higher for those with malignant nodules than for those with benign nodules, even when limited to Lung Computed Tomography Screening Reporting and Data System (LungRADS) category 4 (P &lt; .001).

Conclusions
Circulating protein markers can help differentiate malignant from benign pulmonary nodules. Validation with an independent computed tomographic screening study will be required before clinical implementation.
Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors: existing and emerging differences
Authors: Johnston Stephen , Emde Anna , Barrios Carlos , Srock Stefanie , Neven Patrick , Martin Miguel , Cameron David , Janni Wolfgang , Gnant Michael 
Published: June 2023

AbstractThe cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors palbociclib, ribociclib, and abemaciclib are standard-of-care therapy for hormone receptor-positive advanced or metastatic breast cancer, based on randomized trials showing improved progression-free survival for all 3 drugs and overall survival for ribociclib and abemaciclib. Results in early breast cancer are discordant, with sustained improvement in invasive disease-free survival demonstrated for abemaciclib but not other CDK4/6 inhibitors to date. We review nonclinical studies exploring mechanistic differences between the drugs, the impact of continuous dosing on treatment effect, and translational research into potential resistance mechanisms and prognostic and predictive markers. We focus particularly on how emerging findings may help us understand similarities and differences between the available CDK4/6 inhibitors. Even at late-stage clinical development, there remains much to learn about how agents in this class exert their varying effects.
Reconstruction of cultural memory through digital storytelling: A case study of Shanghai Memory project
Authors: Fu Yaming , Mahony Simon , Liu Wei 
Published: June 2023

Abstract
This article analyses how digital storytelling (DS) is applied to a digital humanities (DH) research project. It considers the purpose of storytelling and illustrates its use to help to democratize the wider project by including diverse voices and helping to reconstruct cultural memory. How can DS be used as a critical research method to help develop a robust methodology in DH research, particularly for organizing historical and cultural resources to form a story world and addressing biases in the established archival collections? This initiative is the latest phase of the Shanghai Memory project, adding an important additional dimension to the established showcase, A Journey from Wukang Road. Wukang Road, with many historical buildings going back to the colonial era, has important cultural significance as part of the former French Concession. Originally known as Rue de Ferguson, the name was changed in 1943, at the time of the Japanese occupation, seemingly as part of anti-colonial sentiment while China was being encouraged to resist her occupiers. Participation in the storytelling project is facilitated by user generated content and promotion in the Shanghai Library. The aim is to present a clearer storyline about the evolution of Wukang Road, explore its historical context, use the stories and reflections of the ordinary people to balance that of the elites, importantly encouraging inclusion of the vernacular Shanghainese dialect as part of wider movements to protect local languages.
High-precision photometric and high-resolution spectroscopic characterization of HD 180347
Authors: Trust Otto , Mashonkina Lyudmila , Jurua Edward , De Cat Peter , Tsymbal Vadim , Joshi Santosh 
Published: June 2023

ABSTRACT
We report the analysis of high-precision space-based photometric and high-resolution spectroscopic observations of HD 180347. The high-quality light curves from the Transiting Exoplanet Survey Satellite (TESS) under sectors 14, 15, and 26 were used. By visual inspection of the light curves and the Fourier transforms, only low-frequency signals (less than 1 d−1) were detected. After using wavelet, autocorrelation, and composite spectrum analyses, HD 180347 is classified as a rotational variable with a period of about 4.1 ± 0.2 d. In reference to the observation limit of TESS, no pulsations were detected. For the spectroscopic analysis, we used data collected with the High Efficiency and Resolution Mercator Échelle Spectrograph (HERMES). We determined the spectral type of this star and obtained atmospheric parameters such as the effective temperature, the surface gravity, and the projected rotational, microturbulent, and radial velocities. We performed a detailed chemical abundance analysis. The LTE abundances were derived for 25 chemical elements. For 13 of them, including Ca, Sc, Sr, Zr, and Ba, which are important for the characterization of chemical peculiarities, we also present the non-local thermodynamic equilibrium (NLTE) abundances. NLTE improves the accuracy of the derived abundances and confirms that Ca and Sc are depleted in HD 180347 relative to their solar abundances, while the heavy elements beyond Sr are enhanced, by more than 0.7 dex. Based on the spectral class and the element abundance pattern, we classify this star as Am (kA1hA8mA8).
The probability of identifying the cosmic web environment of galaxies around clusters motivated by the Weave Wide Field Cluster Survey
Authors: Cornwell Daniel J , Aragón-Salamanca Alfonso , Kuchner Ulrike , Gray Meghan E , Pearce Frazer R , Knebe Alexander 
Published: June 2023

ABSTRACT
Upcoming wide-field spectroscopic surveys will observe galaxies in a range of cosmic web environments in and around galaxy clusters. In this paper, we test and quantify how successfully we will be able to identify the environment of individual galaxies in the vicinity of massive galaxy clusters, reaching out to ∼5R200 into the clusters’ infall region. We focus on the WEAVE Wide Field Cluster Survey (WWFCS), but the methods we develop can be easily generalized to any similar spectroscopic survey. Using numerical simulations of a large sample of massive galaxy clusters from thethreehundred project, we produce mock observations that take into account the selection effects and observational constraints imposed by the WWFCS. We then compare the ‘true’ environment of each galaxy derived from the simulations (cluster core, filament, and neither core nor filament, ‘NCF’) with the one derived from the observational data, where only galaxy sky positions and spectroscopic redshifts will be available. We find that, while cluster core galaxy samples can be built with a high level of completeness and moderate contamination, the filament and NCF galaxy samples will be significantly contaminated and incomplete due to projection effects exacerbated by the galaxies’ peculiar velocities. We conclude that, in the infall regions surrounding massive galaxy clusters, associating galaxies with the correct cosmic web environment is highly uncertain. However, with large enough spectroscopic samples like the ones the WWFCS will provide (thousands of galaxies per cluster, out to 5R200), and the correct statistical treatment that takes into account the probabilities we provide here, we expect we will be able to extract robust and well-quantified conclusions on the relationship between galaxy properties and their environment.
Extravillous trophoblast cell-derived exosomes induce vascular smooth muscle cell apoptosis via a mechanism associated with miR-143-3p
Authors: Liu Hanbo , Chen Miaojuan , Ning Fen , Ye Yixin , Lu Qinsheng , Lu Shenjiao , Duan Yaoyun , Gan Xiaowen , Zhao Mingguang , Guo Kaimin , Lash Gendie E 
Published: June 2023

Abstract
The remodeling of uterine spiral arteries is a complex process requiring the dynamic action of various cell types. During early pregnancy, extravillous trophoblast (EVT) cells differentiate and invade the vascular wall, replacing the vascular smooth muscle cells (VSMCs). Several in vitro studies have shown that EVT cells play an important role in promoting VSMC apoptosis, however, the mechanism underlying this process is not fully understood. In this study, we demonstrated that EVT-conditioned media and EVT-derived exosomes could induce VSMC apoptosis. Through data mining and experimental verification, it was demonstrated that the EVT exosome miR-143-3p induced VSMC apoptosis in both VSMCs and a chorionic plate artery (CPA) model. Furthermore, FAS ligand was also expressed on the EVT exosomes and may play a co-ordinated role in apoptosis induction. These data clearly demonstrated that VSMC apoptosis is mediated by EVT-derived exosomes and their cargo of miR-143-3p as well as their cell surface presentation of FASL. This finding increases our understanding of the molecular mechanisms underlying the regulation of VSMC apoptosis during spiral artery remodeling.
Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data
Authors: Das Subrata , Biswas Nidhan K , Basu Analabha 
Published: June 2023

Abstract
High-throughput sequencing (HTS) has revolutionized science by enabling super-fast detection of genomic variants at base-pair resolution. Consequently, it poses the challenging problem of identification of technical artifacts, i.e. hidden non-random error patterns. Understanding the properties of sequencing artifacts holds the key in separating true variants from false positives. Here, we develop Mapinsights, a toolkit that performs quality control (QC) analysis of sequence alignment files, capable of detecting outliers based on sequencing artifacts of HTS data at a deeper resolution compared with existing methods. Mapinsights performs a cluster analysis based on novel and existing QC features derived from the sequence alignment for outlier detection. We applied Mapinsights on community standard open-source datasets and identified various quality issues including technical errors related to sequencing cycles, sequencing chemistry, sequencing libraries and across various orthogonal sequencing platforms. Mapinsights also enables identification of anomalies related to sequencing depth. A logistic regression-based model built on the features of Mapinsights shows high accuracy in detecting ‘low-confidence’ variant sites. Quantitative estimates and probabilistic arguments provided by Mapinsights can be utilized in identifying errors, bias and outlier samples, and also aid in improving the authenticity of variant calls.
The urine-to-plasma urea concentration ratio is associated with eGFR and eGFR decline over time in a population cohort
Authors: Petrovic Dusan , Bankir Lise , Ponte Belén , Pruijm Menno , Corre Tanguy , Ghobril Jean-Pierre , Bouatou Yassine , Ackermann Daniel , Vogt Bruno , Bochud Murielle 
Published: June 2023

ABSTRACT

Background
Evaluation of renal function and of factors associated with its decline are important public health issues. Besides markers of glomerular function [e.g. glomerular filtration rate (GFR)], those of tubular functions are rarely evaluated. Urea, the most abundant urinary solute, is markedly concentrated in urine when compared with plasma. We explored the urine-to-plasma ratio of urea concentrations (U/P urea ratio) as a marker of tubular functions.

Methods
We evaluated the relationship of the U/P urea ratio with eGFR at baseline in 1043 participants (48 ± 17 years) from the Swiss Kidney Project on Genes in Hypertension (SKIPOGH) population-based cohort, using mixed regression. In 898 participants, we assessed the relation between U/P urea ratio and renal function decline between two study waves 3 years apart. We studied U/P ratios for osmolarity, Na, K and uric acid for comparison.

Results
In a transversal study at baseline, estimated GFR (eGFR) was positively associated with U/P-urea ratio [βscaled = 0.08, 95% CI (0.04; 0.13)] but not with the U/P ratio of osmolarity. Considering separately participants with renal function &gt;90 or ≤90 mL/min × 1.73 m2, this association was observed only in those with reduced renal function. In the longitudinal study, eGFR declined at a mean rate of 1.2 mL/min per year. A significant association was observed between baseline U/P urea ratio and eGFR decline [βscaled = 0.08, 95% CI (0.01; 0.15)]. A lower baseline U/P urea ratio was associated with a greater eGFR decline.

Conclusion
This study provides evidence that the U/P urea ratio is an early marker of kidney function decline in the general adult population. Urea is easy to measure with well-standardized techniques and at low cost. Thus, the U/P urea ratio could become an easily available tubular marker for evaluating renal function decline.
Non-planar dielectrics derived thermal and electrostatic field inhomogeneity for boosted weather-adaptive energy harvesting
Authors: Zhou Yi , Ding Tianpeng , Cheng Yin , Huang Yi , Wang Wu , Yang Jianmin , Xie Lin , Ho Ghim Wei , He Jiaqing 
Published: June 2023

ABSTRACT
Weather-adaptive energy harvesting of omnipresent waste heat and rain droplets, though promising in the field of environmental energy sustainability, is still far from practice due to its low electrical output owing to dielectric structure irrationality and unscalability. Here we present atypical upcycling of ambient heat and raindrop energy via an all-in-one non-planar energy harvester, simultaneously increasing solar pyroelectricity and droplet-based triboelectricity by two-fold, in contrast to conventional counterparts. The delivered non-planar dielectric with high transmittance confines the solar irradiance onto a focal hotspot, offering transverse thermal field propagation towards boosted inhomogeneous polarization with a generated power density of 6.1 mW m−2 at 0.2 sun. Moreover, the enlarged lateral surface area of curved architecture promotes droplet spreading/separation, thus travelling the electrostatic field towards increased triboelectricity. These enhanced pyroelectric and triboelectric outputs, upgraded with advanced manufacturing, demonstrate applicability in adaptive sustainable energy harvesting on sunny, cloudy, night, and rainy days. Our findings highlight a facile yet efficient strategy, not only for weather-adaptive environmental energy recovery but also in providing key insights for spatial thermal/electrostatic field manipulation in thermoelectrics and ferroelectrics.
Prediction in cultured cortical neural networks
Authors: Lamberti Martina , Tripathi Shiven , van Putten Michel J A M , Marzen Sarah , le Feber Joost 
Published: June 2023

Abstract
Theory suggest that networks of neurons may predict their input. Prediction may underlie most aspects of information processing and is believed to be involved in motor and cognitive control and decision-making. Retinal cells have been shown to be capable of predicting visual stimuli, and there is some evidence for prediction of input in the visual cortex and hippocampus. However, there is no proof that the ability to predict is a generic feature of neural networks. We investigated whether random in vitro neuronal networks can predict stimulation, and how prediction is related to short- and long-term memory. To answer these questions, we applied two different stimulation modalities. Focal electrical stimulation has been shown to induce long-term memory traces, whereas global optogenetic stimulation did not. We used mutual information to quantify how much activity recorded from these networks reduces the uncertainty of upcoming stimuli (prediction) or recent past stimuli (short-term memory). Cortical neural networks did predict future stimuli, with the majority of all predictive information provided by the immediate network response to the stimulus. Interestingly, prediction strongly depended on short-term memory of recent sensory inputs during focal as well as global stimulation. However, prediction required less short-term memory during focal stimulation. Furthermore, the dependency on short-term memory decreased during 20 h of focal stimulation, when long-term connectivity changes were induced. These changes are fundamental for long-term memory formation, suggesting that besides short-term memory the formation of long-term memory traces may play a role in efficient prediction.
Memory and Markets
Authors: Kovbasyuk Sergey , Spagnolo Giancarlo 
Published: June 2023

Abstract
In many environments, including credit and online markets, records about participants are collected, published, and erased after some time. We study the effects of erasing past records in a dynamic market where the quality of sellers follows a Markov process, and buyers leave feedback about sellers to an information intermediary. When the average quality of sellers is low, unlimited records lead to a market breakdown in the long run. We consider the information design problem and characterize information policies that can sustain trade and that maximize social welfare. These policies hide some information from the market in order to foster socially desirable experimentation. We show that these outcomes can be implemented by appropriately deleting past records. Crucially, positive and negative records play opposite roles with different intensities and must have different lengths: negative records must be deleted sufficiently late, and positive ones sufficiently early.
Countrywide monitoring of absorbed dose rate in air due to outdoor natural gamma radiation in India
Authors: Mitra Pratip , Mishra Manish K , Reddy Gade Priyanka , Srivastava Saurabh , Salunkhe Sandip S , Kumari Anisha , Gavas Sanjay G , Ninawe Pruthviraj R , Thekkinkattil Mukundan , Garg Saurabh , Kumar Aerattukkara Vinod 
Published: June 2023

Abstract
The Indian Environmental Radiation Monitoring Network continuously monitors, throughout India, the absorbed dose rate in air due to outdoor natural gamma radiation, by using Geiger–Mueller detector-based standalone environmental radiation monitors. The network consists of 546 monitors spread across 91 monitoring locations distributed all over the country. In this paper, the countrywide long-term monitoring results are summarised. The measured mean dose rate of the monitoring locations followed a log-normal distribution and ranged from 50 to 535 nGy.h−1 with a median value of 91 nGy.h−1. Due to outdoor natural gamma radiation, the average annual effective dose was estimated to be 0.11 mSv.y−1.
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
Authors: Kapli Paschalia , Kotari Ioanna , Telford Maximilian J , Goldman Nick , Yang Ziheng 
Published: June 2023

Abstract
Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.