bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suspended-core photonic crystal fibers for SERS detection of biomolecules
Authors: Issatayeva Aizhan , Mariyam Siddra , Kho Kiang Wei , Andersson-Engels Stefan , Cucinotta Annamaria 
Published: January 2025

Abstract
Photonic crystal fiber (PCF) can be used as a microfluidic platform for surface-enhanced Raman spectroscopy (SERS)-based measurement of different samples. PCF can provide a long area of interaction for light, metal nanoparticles (NPs), and analytes incorporated into its holes. This paper provides a COMSOL simulation model for suspended-core PCF used to evaluate the SERS intensity depending on the fiber’s geometry and NPs’ coverage density. The simulation is applied to compare three PCFs with varying sizes and lengths. SERS measurements of adenine and DNA validate the simulation outcomes and demonstrate the potential of PCFs for SERS-based detection of diverse samples.
The effect of travertine waste on the strength and insulation properties of foam concrete
Authors: Guven Huseyin , Inel Mehmet 
Published: January 2025

Abstract
Incorporating waste additives into foam concrete mixtures is a promising route to develop environmentally-friendly concrete production with tailored thermos-mechanical properties. In this paper, the effects of various fabrication parameters of foam concrete, including the type of waste additive, water/binder ratio, density of mixture, and incorporation of glass fibers were investigated. Foam concrete samples were fabricated using fly ash and travertine wastes, and the variations in their compressive strength, and thermal conductivity using various concrete mixture designs were measured. The obtained results show that foam concrete with fly ash additive tends to have higher compressive strength and thermal conductivity than foam concrete with travertine waste. However, the latter exhibits better thermal insulation properties, which tend to improve by adding glass fibers. This work defines the outlines for exploring the use of harmful wastes in fabricating foam concrete. It offers guidelines for developing improved foam concrete mixtures with tailored thermos-mechanical properties.
Simulations of the potential for diffraction enhanced imaging at 8 kev using polycapillary optics
Authors: Bittel Carmen A , MacDonald Carolyn A 
Published: January 2025

Abstract
Conventional x-ray radiography relies on attenuation differences in the object, which often results in poor contrast in soft tissues. X-ray phase imaging has the potential to produce higher contrast but can be difficult to utilize. Instead of grating-based techniques, analyzer-based imaging, also known as diffraction enhanced imaging (DEI), uses a monochromator crystal with an analyzer crystal after the object. Analyzer-based systems most commonly employ synchrotron sources to provide adequate intensity, and typically use higher photon energies. In this work, a simulation has been devised to assess the potential for a polycapillary-based system. A polycapillary collimating optic has previously been shown to greatly enhance the intensity of the beam diffracted from the monochromatizing crystal. Detailed simulation of the optic is computationally intensive and requires comprehensive knowledge of the internal shape of the optic, so a simple geometric model using easier to obtain optic output data was developed and compared to the more detailed simulation. After verification, refraction band visibility was used as a quality parameter to address the effectiveness of the polycapillary-based DEI system at x-ray photon energies of 8 and 17.5 keV. The result shows promise for a polycapillary-coupled analyzer-based system even at low x-ray photon energy.
Security of hybrid BB84 with heterodyne detection
Authors: Sidhu Jasminder S , Maggi Rocco , Pascazio Saverio , Lupo Cosmo 
Published: January 2025

Abstract
Quantum key distribution (QKD) promises everlasting security based on the laws of physics. Most common protocols are grouped into two distinct categories based on the degrees of freedom used to carry information, which can be either discrete or continuous, each presenting unique advantages in either performance, feasibility for near-term implementation, and compatibility with existing telecommunications architectures. Recently, hybrid QKD protocols have been introduced to leverage advantages from both categories. In this work we provide a rigorous security proof for a protocol introduced by Qi in 2021, where information is encoded in discrete variables as in the widespread Bennett Brassard 1984 protocol but decoded continuously via heterodyne detection. Security proofs for hybrid protocols inherit the same challenges associated with continuous-variable protocols due to unbounded dimensions. Here we successfully address these challenges by exploiting symmetry. Our approach enables truncation of the Hilbert space with precise control of the approximation errors and lead to a tight, semi-analytical expression for the asymptotic key rate under collective attacks. As concrete examples, we apply our theory to compute the key rates under passive attacks, linear loss, and Gaussian noise.
Theoretical and experimental analysis of phase noise in semiconductor lasers biased below threshold
Authors: de Zulueta Iker Pascual , Valle Angel 
Published: January 2025

Abstract
We report a theoretical and experimental study of phase noise in semiconductor lasers when the bias current is below the threshold value. The theoretical study is performed by using two types of rate equations, with additive and multiplicative noise terms. We find the conditions for which the evolution in those rate equations can be described by 1-dimensional and two dimensional Brownian motions, respectively. The main statistical differences between the additive and multiplicative noise models are then illustrated by using the simplified Brownian motion models. Additive and multiplicative noise models predictions are compared with measurements of the phase noise with a coherent receiver using a 90∘ optical hybrid. We develop a novel method to extract the phase noise directly from our measurements, that in contrast to the usual direct method is not based on the analysis of the phase noise difference. The method permits a direct visualization of the phase noise trajectories and a calculation of the averages and the distribution that is valid in the short-time limit. Our results are in very good agreement with the results obtained with the method based on the phase noise difference. Our experimental results show that the variance of the phase noise grows linearly in time and has Gaussian statistics, supporting the modelization of the phase noise statistics with the additive noise model.
Dynamic modeling and guidance analysis of a ferromagnetic continuum robot with geometric discretization and base linear motion
Authors: Mallahi Kolahi Pouya , Habibnejad Korayem Moharam 
Published: January 2025

Abstract
With the advancement of robotics in medicine in recent years, diverse and promising applications for ferromagnetic continuum robots (FCRs) have been introduced. These robots utilize an electromagnetic actuation system for movement and control, which leads to reduced tissue damage, significantly shorter surgery durations, and improved patient recovery times. Recent research in FCR modeling highlights the critical challenge of developing a dynamic model to assess system behavior in real-time, crucial for maximizing benefits in medical applications. In this paper, the geometric discretization method and Lagrange’s principle are used to derive the dynamic equations of a FCR under the influence of an external magnetic field. This approach enables the examination of the system’s behavior at any given moment, providing a suitable foundation for designing various controllers based on the model. Given the electromagnetic system used in steering the FCRs, an analysis of the magnetic field in both ideal and real conditions is conducted to enhance reliability for medical applications. Simulation results indicate that the robots deform in a direction different from the magnetic field direction, demonstrating non-planar deformation characteristics. Furthermore, comparison with experimental data demonstrates that the theoretical framework accurately predicts the robot’s deformation, with calculation errors less than 5%.
VirDetect-AI: a residual and convolutional neural network–based metagenomic tool for eukaryotic viral protein identification
Authors: Zárate Alida , Díaz-González Lorena , Taboada Blanca 
Published: January 2025

Abstract
This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.
High-dimensional partially linear functional Cox models
Authors: Chen Xin , Liu Hua , Men Jiaqi , You Jinhong 
Published: January 2025

ABSTRACT
As a commonly employed method for analyzing time-to-event data involving functional predictors, the functional Cox model assumes a linear relationship between the functional principal component (FPC) scores of the functional predictors and the hazard rates. However, in practical scenarios, such as our study on the survival time of kidney transplant recipients, this assumption often fails to hold. To address this limitation, we introduce a class of high-dimensional partially linear functional Cox models, which accommodates the non-linear effects of functional predictors on the response and allows for diverging numbers of scalar predictors and FPCs as the sample size increases. We employ the group smoothly clipped absolute deviation method to select relevant scalar predictors and FPCs, and use B-splines to obtain a smoothed estimate of the non-linear effect. The finite sample performance of the estimates is evaluated through simulation studies. The model is also applied to a kidney transplant dataset, allowing us to make inferences about the non-linear effects of functional predictors on patients’ hazard rates, as well as to identify significant scalar predictors for long-term survival time.
Clinically meaningful eGFR slope as a surrogate endpoint differs across CKD stages and slope evaluation periods: the CKD-JAC study
Authors: Imaizumi Takahiro , Komaba Hirotaka , Hamano Takayuki , Nangaku Masaomi , Murotani Kenta , Hasegawa Takeshi , Fujii Naohiko , Nitta Kosaku , Isaka Yoshitaka , Wada Takashi , Maruyama Shoichi , Fukagawa Masafumi 
Published: January 2025

ABSTRACT

Background
The slope of estimated glomerular filtration rate (eGFR) is a promising surrogate endpoint in patients with chronic kidney disease (CKD). However, current evidence is mainly derived from Western populations with CKD stages 1–3. In addition, stage-by-stage analysis has never been formally performed.

Methods
We analyzed data from the Chronic Kidney Disease Japan Cohort Study, which included a large proportion of patients with CKD stages 4 and 5. We estimated eGFR slopes over three evaluation periods (0.5, 1, and 2 years) using mixed effects models and examined their associations with kidney failure with replacement therapy across CKD stages.

Results
Of 2713 patients with an available 1-year eGFR slope, 985 subsequently initiated kidney replacement therapy. Overall, a slower eGFR decline was strongly associated with a lower risk of subsequent kidney failure with replacement therapy. The association was pronounced with higher baseline CKD stages and attenuated with shorter evaluation periods. The estimated deceleration in eGFR decline over 1 year associated with a 20% lower risk of subsequent kidney failure with replacement therapy was 1.91 (1.60–2.37), 1.12 (1.00–1.28), and 1.06 (0.81–1.60) ml/min/1.73 m2 per year in patients with CKD stages 3, 4, and 5, respectively.

Conclusion
Our results support the potential of eGFR slope as a surrogate across different stages of CKD in Asians and suggest that a shorter evaluation period than 2 years may be feasible for patients with late-stage CKD. Our findings provide valuable insights for the future design of clinical trials in CKD patients, especially those with more advanced CKD.
Imaging-based method to quantify left ventricular diastolic pressures
Authors: Smiseth Otto A , Fernandes Joao F , Ohte Nobuyuki , Wakami Kazuaki , Donal Erwan , Remme Espen W , Lamata Pablo 
Published: January 2025

Abstract

Aim
To establish an imaging-based method to quantify left ventricular (LV) diastolic pressures.

Methods/results
In 115 patients suspected of coronary artery disease, LV pressure was measured by micromanometers and images by echocardiography. LV filling pressure was measured as LV pre-atrial contraction pressure (pre-A PLV). Based on previous observations we hypothesized that pre-A PLV approximates the sum of minimum PLV and maximum transmitral pressure difference. Parameters used for pressure estimates included LV volumes and strain, left atrial strain, mitral flow velocities, systolic arterial cuff pressure and body mass index. Minimum PLV was estimated by predictors identified in a derivative cohort (n=81). Mitral pressure difference was calculated by a simplified Navier-Stokes equation. Accuracy of estimates of minimum PLV, pre-A PLV and end-diastolic PLV were investigated in a testing cohort (n=19). Patient-specific LV diastolic pressure curves were constructed by adjusting a reference curve according to pressure estimates at key diastolic events.
There was good agreement between estimated and measured pre-A PLV: Bias 0.0, limits of agreement &lt;3.1 mmHg (±1.96SD). Estimated minimum PLV and end-diastolic PLV also showed good agreement with measured pressures. Furthermore, there was good agreement between measured and estimated LV diastolic pressure curves, quantified as mean LV diastolic pressure: Bias 0.2, limits of agreement &lt;3.2 mmHg.

Conclusion
The proposed non-invasive method provided estimates of minimum PLV, pre-A PLV and end-diastolic PLV, each reflecting different features of diastolic function. Additionally, it provided an estimate of the LV diastolic pressure curve. Validation in larger populations with different phenotypes is necessary to determine the validity of the method in clinical practice.
Invading and range-expanding pink salmon inform management actions for marine species on the move
Authors: Dunmall Karen M , Bean Colin W , Berntsen Henrik H , Ensing Dennis , Erkinaro Jaakko , Irvine James R , Kendall Neala W , Kitching Tor , Langan Joseph A , Millane Michael , Oxman Dion S , Radchenko Vladimir I , Thorstad Eva B , Utne Kjell Rong 
Published: January 2025

Abstract
Species redistributions, whether resulting from invasions or range expansions, pose similar challenges for conservation and management. Redistribution impacts on host ecosystems and species combine with those from climate change, which are already acute at northern latitudes. Using pink salmon Oncorhynchus gorbuscha, which are native to the Pacific Ocean, we employ knowledge exchange to inform decision-making in non-native marine areas: they are expanding their range to the Arctic Ocean and are invasive in the Atlantic Ocean. The predicted future marine distribution of pink salmon focuses effort on where and when pink salmon are present and informs on potential interactions with native species. Management actions taken in the Atlantic Ocean to reduce invasive pink salmon are resource-intensive, but removed salmon could be a food resource. Addressing identified gaps regarding the invasion potential of pink salmon, interactions among pink salmon and other species, and current mitigation efforts would support forward-thinking management decisions given predictions of continued environmental change. We also highlight steps that can be taken immediately to coordinate actions and better inform responses. Managed for production in the Pacific and as an invasion in the Atlantic, pink salmon provide a tangible approach to informed decision-making through collaboration for marine species on the move.
Argos satellite transmitters enable billfish research at finer scales
Authors: Arostegui Martin C , Gaube Peter , Vo Amie , Thorrold Simon R , Braun Camrin D 
Published: January 2025

Abstract
Satellite transmitters that provide Doppler-based locations and telemeter data via the Argos satellite system have revealed a wealth of information on the movement ecology of diverse fauna such as marine mammals, turtles, and sharks. In contrast, satellite telemetry studies of bony fishes have almost exclusively relied on pop-up satellite archival tags (PSATs) that use light-based geolocation to estimate movements. However, track reconstructions based on light and other sensor data transmitted by PSATs exhibit positional error that is orders of magnitude higher than those from Argos Doppler-based locations, effectively limiting our understanding of bony fish movement ecology to coarse scales. Although PSATs continue to be the technological workhorse of billfish research, with more than 1000 data records published to date, a handful of pioneering studies have tried using tags capable of providing Argos Doppler-based locations to better understand these taxa. We assess the applicability of Argos satellite transmitters to study billfish in the context of their depth distribution and by comparing alternative tag attachment strategies and form factors. We present two case studies that highlight how these data can explicitly be used for fine-scale ecological and oceanographic research. This work culminates with the introduction of a new Smart Position and Temperature (SPOT) transmitting tag designed specifically for billfish and other pelagic fishes that has the potential to open new avenues of research, revealing dimensions of behavior that previously could not be investigated.
Proteins and pathways involved in inflammation are longitudinally associated with total body bone mineral density among primarily Hispanic overweight/obese adolescents and young adults
Authors: Beglarian Emily , Chen Jiawen Carmen , Li Zhenjiang , Costello Elizabeth , Wang Hongxu , Hampson Hailey , Alderete Tanya L , Chen Zhanghua , Valvi Damaskini , Rock Sarah , Chen Wu , Rianon Nahid , Aung Max T , Gilliland Frank D , Goran Michael I , McConnell Rob , Eckel Sandrah P , Lee Miryoung , Conti David V , Goodrich Jesse A , Chatzi Lida 
Published: January 2025

Abstract
BMD, an important marker of bone health, is regulated by a complex interaction of proteins. Plasma proteomic analyses can contribute to identification of proteins associated with changes in BMD. This may be especially informative in stages of bone accrual and peak BMD achievement (ie, adolescence and young adulthood), but existing research has focused on older adults. This analysis in the Study of Latino Adolescents at Risk for Type 2 Diabetes (SOLAR; n = 304; baseline age 8-13, 100% Hispanic) explored associations between baseline proteins (n = 653 proteins) measured with Olink plasma protein profiling and repeated annual DXA measures of BMD (average of 3.2 visits per participant). Covariate-adjusted linear mixed effect regression models were applied to estimate longitudinal protein—BMD associations using an adjusted p value cutoff (p &lt; .00068). Identified proteins were imported into the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database to determine significantly enriched protein pathways. Forty-four proteins, many of which are involved in inflammatory processes, were associated with longitudinal changes in total body BMD, including several proteins previously linked to bone health such as osteopontin (SPP1) and microfibrillar-associated protein 5 (MFAP5; both p &lt; .00068). These 44 proteins were associated with enrichment of pathways including PI3K-Akt signaling pathway and cytokine–cytokine receptor interaction, supporting results from existing proteomics analyses in older adults. To evaluate whether protein associations were consistent into young adulthood, linear mixed effect models were repeated in a young adult cohort (n = 169; baseline age 17-22; 62.1% Hispanic) with 346 available overlapping Olink protein measures. While there were no significant overlapping longitudinal protein associations between the cohorts, these findings suggest differences in protein regulation at different ages and provide novel insight on longitudinal protein associations with BMD in overweight/obese adolescents and young adults of primarily Hispanic origin, which may inform the development of biomarkers for bone health in youth.
Presidential Address 2024: The Value and Profits of Firms
Authors: Eeckhout Jan 
Published: January 2025

Abstract
The real growth of the stock market value of firms has increased from close to 0% on average per year between 1958 and 1980, to 5.2% between 1980 and today. This change coincides with the rise of market power and profits, starting in 1980. This paper proposes to decompose the value of firms based on profits (earnings) rather than dividends. Because firms on average pay out only half of profits in dividends, dividends poorly measure firm performance. I decompose the sources of the rise of the value of all publicly traded firms into the following categories: (1) the subjective and risk-free discount factor, (2) expected future profits, and (3) shareholder equity (retained earnings). I find that 20% of the rise is due to the discount factor and 80% is due to profits (45% current and future expected profits; 35% retained earnings). I build a general equilibrium model of the economy where firms have market power; I perform counterfactuals and evaluate the welfare implications. The objective is to study the impact of competition policy. If market power today dropped to the level of 1980, average stock market values would be 45% lower. Instead, if market power had never increased in 1980, the average stock values would be 80% lower.
Rationally Inattentive Statistical Discrimination: Arrow Meets Phelps
Authors: Echenique Federico , Li Anqi 
Published: January 2025

Abstract
When information acquisition is costly but flexible, a principal may rationally acquire information that favors one group over another. The former group faces incentives to invest in becoming productive, while the latter is discouraged from such investments. In turn, the principal largely overlooks the productivity differences between groups and primarily promotes the invested group, unless the underinvested group surprises him with a genuinely outstanding outcome. We show that, when attention costs are intermediate, investment costs are low, and investments are likely to succeed, the discriminatory equilibrium is the most preferred by the principal, despite all groups being ex-ante identical. Our results inform the discussion of affirmative action, implicit bias, and occupational segregation and stereotypes.