bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the effects of bioinspired vortex generators on aerodynamic performance of a NACA0015 airfoil
Authors: Kaya Fatih , Akbıyık Hürrem 
Published: December 2024

Abstract
An experimental study was carried out to investigate the effects of biomimetic vortex generators (biomimetic-VGs) on the aerodynamic performance of the NACA0015 airfoil. Aerodynamic force measurements and titanium dioxide (TiO2) based flow visualization technique experiments were performed for test models at Re = 1.2 × 105. Aerodynamic force measurement experiments were carried out in the wind tunnel at angles of attack of 0°–18° with an increment of 1°. As a result of the experiments, it was revealed that the lift coefficient (C
L) increased and the drag coefficient (C
D) decreased by using the seaconchshell structure as a VG for the wing model. In addition, it has been observed that biomimetic models (BMs) shifted the stall angle of the airfoil by 1°. In the surface oil flow visualization experiment results, the flow structure around the NACA0015 airfoil of BMs was revealed and interpreted. Moreover, it has been revealed that the aerodynamic performance of the airfoil increases as a result of the use of BMs. It is also revealed that the seaconchshell structure, which has not been studied before in the literature and which is the subject of this study, can be used as an effective flow control device.
A local meteoric water line for interior Alaska constrains paleoclimate from 40 000 year old relict permafrost
Authors: Douglas Thomas A , Barker Amanda J , Monteath Alistair J , Froese Duane G 
Published: December 2024

Abstract
Anthropogenic climate warming is degrading permafrost across interior Alaska. Information from past warming events provides long-term perspectives for future trajectories; however, late Quaternary seasonal temperatures are poorly constrained. We have established a stable water isotope meteoric water line for interior Alaska and measured stable water isotope values from 126 permafrost cores representing different ice types deposited over the past ∼40 ka (thousand years before 1950 CE). Samples represent two late Quaternary warm periods: marine isotope stage three (MIS3; 57–29 ka) and the Holocene (11.7 ka-present). Older samples provide insight into local climatic conditions slightly before the first archeological evidence for Paleolithic hunter-gatherers in the region. From permafrost ice we calculate that summer temperatures warmed by ∼10 °C between late MIS3 and today, with six degrees of warming between 40–30 ka and 3 ka and an additional 4 °C of warming since 3 ka. Half this recent 4 °C warming has occurred over the past 70 years.
Continual Developmental Neurosimulation Using Embodied Computational Agents
Authors: Alicea B , Chakrabarty R , Dvoretskii S , Gopiiswaminathan AV , Lim A , Parent J 
Published: December 2024

Abstract
There is much to learn through synthesis of Developmental Biology, Cognitive Science and Computational Modeling. Our path forward is to present a design for developmentally-inspired learning agents based on Braitenberg Vehicles. Using these agents to exemplify the embodied nature of computational autonomy, we move closer to modeling embodied experience and morphogenetic growth as components of cognitive developmental capacity. We consider biological and cognitive development which influence the generation of adult phenotypes and the contingency of available developmental pathways. Continual developmental neurosimulation allows us to consider the role of developmental trajectories in bridging the related phenomena of nervous system morphogenesis, developmental learning, and plasticity. Being closely tied to continual learning, our approach is tightly integrated with developmental embodiment, and can be implemented using a type of agent called developmental Braitenberg Vehicles (dBVs). dBVs begin their lives as a set of undefined structures that transform into agent-based systems including a body, sensors, effectors, and nervous system. This phenotype is characterized in terms of developmental timing: with distinct morphogenetic, critical, and acquisition (developmental learning) periods. These properties produce emergent connectivity with shifting weights and adaptive network topologies in the context of developmental processes and spatially-dependent embodiment in training a dBVs neuronal network. We further propose that network morphogenesis can be accomplished using a genetic algorithmic approach, while developmental learning can be implemented using a number of computational methodologies. This approach provides a framework for adaptive agent behavior that might result from a developmental approach: namely by exploiting critical periods or growth and acquisition, an explicitly embodied network architecture, and a distinction between the assembly of neuronal networks and active learning on these networks. In conclusion, we will consider agent learning and development at different timescales, from very short (<100ms) intervals to long-term evolution. The development, evolution, and learning in an embodied agent-based approach is key to an integrative view of biologically-inspired intelligence.
Optical skyrmions in nonlinear birefringence media: semiclassical approach incorporating effective gauge field
Authors: Kuratsuji Hiroshi 
Published: December 2024

Abstract
A theoretical study is presented for the optical skyrmion (or optical spin vortex) which is expected to occur in nonlinear birefringence media. This is investigated from the aspect of the quantum spinor condensate, whose order parameter is given by the photon field (vector potential). The procedure is based on an extended paraxial approximation; namely, the low-energy oscillation amplitude of the vector potential is decoupled from the high-frequency part. The result is the (2+1) field theory, which is described by a two-component spinor and is expressed in terms of the Stokes parameters. First, we consider the skyrmion for the case of a pure photon field. There are two specific topics: one concerns the polarization singularity, which is a trajectory of the center line of the skyrmion, called the ‘C-line’, which means the trajectory of circular polarization. The other is semiclassical quantization, which is derived for the equation of motion of the vortex (or skyrmion) center. Here, a brief comment is given for an analogy with the Hall effect occurring in the superconductivity vortex. The theory is extended such that the photon field allows a coupling with an effective gauge field. We examine the skyrmion–gauge field coupling from two aspects: one is strong coupling, in which the gauge field acts so as to stabilize the skyrmion. The other is weak coupling, for which the interaction between the gauge phonon and skyrmion motion is treated by a perturbation scheme, which provides the basis for the possible detection of gauge phonons.
A perspective on suspended membrane waveguides for gas sensing applications in mid-infrared spectrum
Authors: Butt Muhammad Ali 
Published: December 2024

Abstract
Suspended membrane waveguides (SMWs) are crucial for sensing in the mid-infrared (MIR) spectrum due to their exceptional ability to confine light within an ultra-thin dielectric core supported by the membrane, enhancing sensitivity to environmental changes. Properly designed SMWs exhibit minimal optical losses and strong mode confinement, enabling them to maintain high performance even at longer MIR wavelengths, unlike ridge, slot, and subwavelength grating waveguides. This is particularly important for chemical and biological sensing, where precise detection of molecular vibrations in the MIR range is vital. Additionally, the open geometry of suspended membranes allows for better interaction between the guided light and surrounding analytes, leading to improved sensing efficiency and lower limit of detection. These unique characteristics make SMWs especially advantageous for advanced MIR sensing applications.
AI-enhanced interface for colonic polyp segmentation using DeepLabv3+ with comparative backbone analysis
Authors: Oğuz Faruk Enes , Alkan Ahmet 
Published: December 2024

Abstract
Polyps are one of the early stages of colon cancer. The detection of polyps by segmentation and their removal by surgical intervention is of great importance for making treatment decisions. Although the detection of polyps through colonoscopy images can lead to multiple expert needs and time losses, it can also include human error. Therefore, automatic, fast, and highly accurate segmentation of polyps from colonoscopy images is important. Many methods have been proposed, including deep learning-based approaches. In this study, a method using DeepLabv3+ with encoder-decoder structure and ResNet architecture as backbone network is proposed for the segmentation of colonic polyps. The Kvasir-SEG polyp dataset was used to train and test the proposed method. After images were preprocessed, the training of the proposed network was performed. The trained network was then tested and performance metrics were calculated, and additionally, a GUI (Graphical User Interface) was designed to enable the segmentation of colonoscopy images for polyp segmentation. The experimental results showed that the ResNet-50 based DeepLabv3+ model had high performance metrics such as mean DSC: 0.9873, mean IoU: 0.9751, demonstrating its effectiveness in the segmentation of colonic polyps. In conclusion, our method utilizing DeepLabv3+ with a ResNet-50 backbone achieves highly accurate colonic polyp segmentation. The obtained results demonstrate its potential to significantly enhance colorectal cancer diagnosis and planning for polypectomy surgery through automated image analysis.
Profiling quantum circuits for their efficient execution on single- and multi-core architectures
Authors: Bandic Medina , le Henaff Pablo , Ovide Anabel , Escofet Pau , Ben Rached Sahar , Rodrigo Santiago , van Someren Hans , Abadal Sergi , Alarcón Eduard , Almudever Carmen G , Feld Sebastian 
Published: December 2024

Abstract
Application-specific quantum computers offer the most efficient means to tackle problems intractable by classical computers. Realizing these architectures necessitates a deep understanding of quantum circuit properties and their relationship to execution outcomes on quantum devices. Our study aims to perform for the first time a rigorous examination of quantum circuits by introducing graph theory-based metrics extracted from their qubit interaction graph and gate dependency graph (GDG) alongside conventional parameters describing the circuit itself. This methodology facilitates a comprehensive analysis and clustering of quantum circuits. Furthermore, it uncovers a connection between parameters rooted in both qubit interaction and GDGs, and the performance metrics for quantum circuit mapping, across a range of established quantum device and mapping configurations. Among the various device configurations, we particularly emphasize modular (i.e. multi-core) quantum computing architectures due to their high potential as a viable solution for quantum device scalability. This thorough analysis will help us to: i) identify key attributes of quantum circuits that affect the quantum circuit mapping performance metrics; ii) predict the performance on a specific chip for similar circuit structures; iii) determine preferable combinations of mapping techniques and hardware setups for specific circuits; and iv) define representative benchmark sets by clustering similarly structured circuits.
Delineating potential sites for Natech due to climate change in the Selangor River Basin, Malaysia
Authors: Yahaya Nurul Syazwani , Pereira Joy Jacqueline , Taha Mohd Raihan , Yaacob Wan Zuhairi Wan 
Published: December 2024

Abstract
Climate change is expected to result in intensifying extreme weather that would increase the risks of climate hazards; leading to natural hazards triggering technological disasters (Natech) events. This paper highlights a simple method using easily available information to identify potential sites for Natech associated with climate change based on a case study of the Selangor River Basin in Malaysia. The approach draws heavily on susceptibility modelling, in combination with screening processes to delineate exposed potential point sources, followed by field inspection to validate the information. Findings reveal that with the onset of climate change, over 55% of the manufacturing industries in the Selangor River Basin are exposed to the risk of Natech due to floods and coastal inundation. The approach can be applied to river basins where industrial activities are prevalent and local information on future climate conditions is limited. It is useful for raising awareness, providing early warning of emerging hazards in worst-case scenarios, and prioritizing climate actions on Natech risk due to climate change.
Non-Fatal Suicidal Self-Directed Violence among U.S. Veterans (2022): The Assessing Social and Community Environments with National Data (ASCEND) for Veteran Suicide Prevention Study
Authors: Hoffmire Claire A , Barnes Sean M , Holliday Ryan , Kittel Julie A , Schneider Alexandra L , Brenner Lisa A , Tock Jamie L , Monteith Lindsey L 
Published: December 2024

Abstract
From 2001-2021, the age- and sex-adjusted Veteran suicide rate increased 76.3%. Surveillance of suicidal ideation (SI) and non-fatal suicidal self-directed violence (NF-SSDV) is a critical component of public health-oriented suicide prevention efforts. To facilitate national NF-SSDV surveillance, a biennial, population-based survey was initiated: Assessing Social and Community Environments with National Data (ASCEND) for Veteran Suicide Prevention. 17,396 Veterans participated in the first large-scale ASCEND survey (2022). This manuscript reports on SI and NF-SSDV prevalence among Veterans residing in the continental U.S., Hawaii, and Puerto Rico. Lifetime SI was reported by 31.98% (95%CI=30.97-32.99), post-military SI by 25.88% (95%CI=24.91-26.85) and past-year SI by 12.69% (95%CI=11.90-13.47). The most commonly considered SI method among those with past-year SI was gunshot. Additionally, 34.42% (95%CI=33.07-35.78) of Veterans with lifetime SI reported lifetime preparatory behaviors. Moreover, 9.13% (95%CI=8.43-9.82) of Veterans reported lifetime interrupted attempts. Lifetime suicide attempts (SA) were reported by 6.99% (95%CI=6.41-7.56) of Veterans, with 4.88% (95%CI=4.39-5.36) reporting post-military SA. The most common method in prior attempts was medication overdose. ASCEND provides a novel opportunity to elucidate the prevalence of SI and different types of NF-SSDV in the Veteran population. Recurring administration will elucidate changes in SI and NF-SSDV prevalence in the Veteran population over time.
Transcriptomic analysis reveals 3 important carbohydrate-active enzymes contributing to starch degradation of the oleaginous yeast Lipomyces starkeyi
Authors: Mine Kentaro , Taki Hiroya , Kim Juyoung , Seto Jiro , Matsuo Shinji , Sato Rikako , Takaku Hiroaki 
Published: December 2024

Abstract
The oleaginous yeast Lipomyces starkeyi has a high capacity for starch assimilation, but the genes involved and specific mechanisms in starch degradation remain unclear. This study aimed to identify the critical carbohydrate-active enzyme (CAZyme) genes contributing to starch degradation in L. starkeyi. Comparative transcriptome analysis of cells cultured in glucose and soluble starch medium revealed that 55 CAZymes (including transcript IDs 3772, 1803, and 7314) were highly expressed in soluble starch medium. Protein domain structure and disruption mutant analyses revealed that 3772 encodes the sole secreted α-amylase (LsAmy1p), whereas 1803 and 7314 encode secreted α-glucosidase (LsAgd1p and LsAgd2p, respectively). Triple-gene disruption exhibited severely impaired growth in soluble starch, dextrin, and raw starch media, highlighting their critical role in degrading polysaccharides composed of glucose linked by α-1,4-glucosidic bonds. This study provided insights into the complex starch degradation mechanism in L. starkeyi.
The Naïve Bayes classifier++ for metagenomic taxonomic classification—query evaluation
Authors: Duan Haozhe (Neil) , Hearne Gavin , Polikar Robi , Rosen Gail L 
Published: December 2024

Abstract

Motivation
This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

Results
NBC++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.

Availability and implementation
Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.
18F-PI-2620 Tau PET is associated with cognitive and motor impairment in Lewy body disease
Authors: Winer Joseph R , Vossler Hillary , Young Christina B , Smith Viktorija , Romero America , Shahid-Besanti Marian , Abdelnour Carla , Wilson Edward N , Anders David , Pacheco Morales Aimara , Andreasson Katrin I , Yutsis Maya V , Henderson Victor W , Davidzon Guido A , Mormino Elizabeth C , Poston Kathleen L 
Published: December 2024

Abstract
Co-pathology is frequent in Lewy body disease, which includes clinical diagnoses of both Parkinson’s disease and dementia with Lewy bodies. Measuring concomitant pathology in vivo can improve clinical and research diagnoses and prediction of cognitive trajectories. Tau PET imaging may serve a dual role in Lewy body disease by measuring cortical tau aggregation as well as assessing dopaminergic loss attributed to binding to neuromelanin within substantia nigra. We sought to characterize 18F-PI-2620, a next generation PET tracer, in individuals with Lewy body disease. We recruited 141 participants for 18F-PI-2620 PET scans from the Stanford Alzheimer’s Disease Research Center and the Stanford Aging and Memory Study, most of whom also had β-amyloid status available (139/141) from PET or cerebrospinal fluid. We compared 18F-PI-2620 uptake within entorhinal cortex, inferior temporal cortex, precuneus and lingual gyrus, as well as substantia nigra, across participants with Lewy body disease [Parkinson’s disease (n = 29), dementia with Lewy bodies (n = 14)] and Alzheimer’s disease (n = 28), in addition to cognitively unimpaired healthy older adults (n = 70). Mean bilateral signal was extracted from cortical regions of interest in 18F-PI-2620 standard uptake value ratio (inferior cerebellar grey reference) images normalized to template space. A subset of participants received cognitive testing and/or the Movement Disorders Society Unified Parkinson’s Disease Rating Scale Part III motor exam (off medication). 18F-PI-2620 uptake was low overall in Lewy body disease and correlated with β-amyloid PET in temporal lobe regions and precuneus. Moreover, inferior temporal 18F-PI-2620 uptake was significantly elevated in β-amyloid positive relative to β-amyloid negative participants with Lewy body disease. Temporal lobe 18F-PI-2620 signal was not associated with memory in Lewy body disease, but uptake within precuneus and lingual gyrus was associated with worse executive function and attention/working memory performance. Finally, substantia nigra 18F-PI-2620 signal was significantly reduced in participants with Parkinson’s disease, and lower substantia nigra signal was associated with greater motor impairment. These findings suggest that although levels are lower than in Alzheimer’s disease, small elevations in cortical tau are associated with cognitive function in Lewy body disease relevant domains, and that reduced 18F-PI-2620 binding in substantia nigra may represent loss of dopaminergic neurons. Cortical tau and neuromelanin binding within substantia nigra represent two unique signals in the same PET image that may be informative in the context of cognitive and motor deficits, respectively, in Lewy body disease.
Experimental determination of deviation from spherical electron densities of atoms in cyclohexane molecules in the liquid state
Authors: Kameda Yasuo , Takaku Akane , Amo Yuko , Usuki Takeshi , Nawa Kazuhiro , Sato Taku J , Honda Takashi , Otomo Toshiya 
Published: December 2024

Abstract
Deviation from the spherical electron distribution of atoms in liquid cyclohexane has been determined through the difference interference term between the observed x-ray intermolecular interference term and the sum of the intermolecular partial structure factors weighted by x-ray atomic scattering factors. The difference distribution function indicates a broadened negative peak at r ∼ 3.7 Å, suggesting that the electron density decreases in the radial distance that corresponds to the intermolecular distances of neighboring cyclohexane molecules.
Collagen type III formation but not degradation is associated with risk of kidney disease progression and mortality after acute kidney injury
Authors: Sparding Nadja , Genovese Federica , Karsdal Morten Asser , Selby Nicholas M 
Published: December 2024

ABSTRACT

Background
Acute kidney injury (AKI), a rapid decrease in kidney function, is associated with increased risk of adverse outcomes including development and progression of CKD. Kidney fibrosis is one of the pathological processes central to this AKI-to-CKD transition. Here we investigate the association of biomarkers of collagen type III turnover with adverse outcome following AKI.

Methods
We measured three biomarkers reflecting collagen type III (PRO-C3) formation and degradation (C3M and C3C) in plasma samples collected 1 year after an episode of AKI in 800 patients (392 patients with AKI and 408 non-AKI controls) from the prospective AKI Risk in Derby (ARID) study. Patients were followed until 3 years after the episode of AKI and the following outcomes were assessed: kidney disease progression, mortality, heart failure, cardiovascular events, and hospital readmission.

Results
PRO-C3 levels were elevated in the AKI group compared with the controls (P &lt; .001), whereas C3M and C3C levels were not different between groups. In multivariate models including common risk factors, PRO-C3 was prognostic for kidney disease progression and mortality in the AKI group and for heart failure in the control group. C3M and C3C were not prognostic for any of the investigated outcomes.

Conclusions
Circulating PRO-C3, a biomarker of fibroblast activity, was prognostic for kidney disease progression and mortality when measured 1 year after an episode of AKI. Biomarkers of fibroblast activity may help patient stratification after an episode of AKI by identifying patients at higher risk of kidney disease progression.