bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutralizing antibody immune correlates in COVAIL trial recipients of an mRNA second COVID-19 vaccine boost
Authors: Zhang Bo , Fong Youyi , Dang Lauren , Fintzi Jonathan , Chen Shiyu , Wang Jing , Rouphael Nadine G. , Branche Angela R. , Diemert David J. , Falsey Ann R. , Graciaa Daniel S. , Baden Lindsey R. , Frey Sharon E. , Whitaker Jennifer A. , Little Susan J. , Kamidani Satoshi , Walter Emmanuel B. , Novak Richard M. , Rupp Richard , Jackson Lisa A. , Yu Chenchen , Magaret Craig A. , Molitor Cindy , Borate Bhavesh , Busch Sydney , Benkeser David , Netzl Antonia , Smith Derek J. , Babu Tara M. , Kottkamp Angelica C. , Luetkemeyer Anne F. , Immergluck Lilly C. , Presti Rachel M. , Bäcker Martín , Winokur Patricia L. , Mahgoub Siham M. , Goepfert Paul A. , Fusco Dahlene N. , Atmar Robert L. , Posavad Christine M. , Mu Jinjian , Makowski Mat , Makhene Mamodikoe K. , Nayak Seema U. , Roberts Paul C. , Gilbert Peter B. , Follmann Dean ,   Coronavirus Variant Immunologic Landscape Trial (COVAIL) Study Team
Published: January 2025

Abstract
Neutralizing antibody titer has been a surrogate endpoint for guiding COVID-19 vaccine approval and use, although the pandemic’s evolution and the introduction of variant-adapted vaccine boosters raise questions as to this surrogate’s contemporary performance. For 985 recipients of an mRNA second bivalent or monovalent booster containing various Spike inserts [Prototype (Ancestral), Beta, Delta, and/or Omicron BA.1 or BA.4/5] in the COVAIL trial (NCT05289037), titers against 5 strains were assessed as correlates of risk of symptomatic COVID-19 (“COVID-19”) and as correlates of relative (Pfizer-BioNTech Omicron vs. Prototype) booster protection against COVID-19 over 6 months of follow-up during the BA.2-BA.5 Omicron-dominant period. Consistently across the Moderna and Pfizer-BioNTech vaccine platforms and across all variant Spike inserts assessed, both peak and exposure-proximal (“predicted-at-exposure”) titers correlated with lower Omicron COVID-19 risk in individuals previously infected with SARS-CoV-2, albeit significantly less so in naïve individuals [e.g., exposure-proximal hazard ratio per 10-fold increase in BA.1 titer 0.74 (95% CI 0.59, 0.94) for naïve vs. 0.41 (95% CI 0.23, 0.64) for non-naïve; interaction p = 0.013]. Neutralizing antibody titer was a strong inverse correlate of Omicron COVID-19 in non-naïve individuals and a weaker correlate in naïve individuals, posing questions about how prior infection alters the neutralization correlate.
Anti-correlation of LacI association and dissociation rates observed in living cells
Authors: Kandavalli Vinodh , Zikrin Spartak , Elf Johan , Jones Daniel 
Published: January 2025

Abstract
The rate at which transcription factors (TFs) bind their cognate sites has long been assumed to be limited by diffusion, and thus independent of binding site sequence. Here, we systematically test this assumption using cell-to-cell variability in gene expression as a window into the in vivo association and dissociation kinetics of the model transcription factor LacI. Using a stochastic model of the relationship between gene expression variability and binding kinetics, we performed single-cell gene expression measurements to infer association and dissociation rates for a set of 35 different LacI binding sites. We found that both association and dissociation rates differed significantly between binding sites, and moreover observed a clear anticorrelation between these rates across varying binding site strengths. These results contradict the long-standing hypothesis that TF binding site strength is primarily dictated by the dissociation rate, but may confer the evolutionary advantage that TFs do not get stuck in near-operator sequences while searching.
Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences
Authors: Velsko Irina M. , Warinner Christina 
Published: January 2025

Abstract
The genus Streptococcus is highly diverse and a core member of the primate oral microbiome. Streptococcus species are grouped into at least eight phylogenetically-supported clades, five of which are found almost exclusively in the oral cavity. We explored the dominant Streptococcus phylogenetic clades in samples from multiple oral sites and from ancient and modern-day humans and non-human primates and found that clade dominance is conserved across human oral sites, with most Streptococcus reads assigned to species falling in the Sanguinis or Mitis clades. However, minor differences in the presence and abundance of individual species within each clade differentiated human lifestyles, with loss of S. sinensis appearing to correlate with toothbrushing. Of the non-human primates, only baboons show clade abundance patterns similar to humans, suggesting that a habitat and diet similar to that of early humans may favor the growth of Sanguinis and Mitis clade species.
An image dataset for surveillance of personal protective equipment adherence in healthcare
Authors: Yang Wanzhao , Kim Mary S. , Sippel Genevieve J. , Mun Aaron H. , McCarthy Kathleen H. , Park Beomseok , Sarcevic Aleksandra , Linguraru Marius George , Marsic Ivan , Burd Randall S. 
Published: January 2025

Abstract
Proper personal protective equipment (PPE) use is critical to prevent disease transmission to healthcare providers, especially those treating patients with a high infection risk. To address the challenge of monitoring PPE usage in healthcare, computer vision has been evaluated for tracking adherence. Existing datasets for this purpose, however, lack a diversity of PPE and nonadherence classes, represent single not multiple providers, and do not depict dynamic provider movement during patient care. We introduce the Resuscitation Room Personal Protective Equipment (R2PPE) dataset that bridges this gap by providing a realistic portrayal of diverse PPE use by multiple interacting individuals in a healthcare setting. This dataset contains 26 videos, 10,034 images and 123,751 bounding box annotations for 17 classes of PPE adherence and nonadherence for eyewear, masks, gowns, and gloves, and one additional head class. Evaluations using newly proposed metrics confirm R2PPE exhibits higher annotation density than three established general-purpose and medical PPE datasets. The R2PPE dataset provides a resource for developing computer vision algorithms for monitoring PPE use in healthcare.
Enhancing energy autonomy of greenhouses with semi-transparent photovoltaic systems through a comparative study of battery storage systems
Authors: Gholami Mohammadreza , Arefi Ali , Hasan Anwarul , Li Chengdao , Muyeen S. M. 
Published: January 2025

Abstract
Effective energy management is crucial in greenhouse farming to ensure efficient operations and optimal crop growth. This study investigates the energy autonomy—defined as the ratio of on-site energy generation to the total energy demand—of greenhouses equipped with semi-transparent photovoltaic (STPV) systems under two scenarios: with and without a Battery Energy Storage System (BESS). STPV systems are beneficial because they generate energy while still allowing enough light to pass through for healthy plant development. Seasonal variations in energy autonomy during summer and winter were analyzed. Results show that incorporating BESS significantly reduces reliance on grid electricity, with energy autonomy improving from 43.43% to 24.17% in summer and 81.36% to 69.45% in winter. The system’s performance was highly sensitive to the transmittance rate of STPV panels and the minimum Daily Light Integral (DLI) required for crops. These findings highlight the potential of BESS to enhance energy independence and promote sustainable agricultural practices. The study provides insights into optimizing renewable energy systems in greenhouses, emphasizing practical implications for scalability and economic feasibility.
Spatial analysis and risk mapping of Crimean-Congo hemorrhagic fever (CCHF) in Sub-saharan Africa
Authors: Ilboudo Abdoul Kader , Oloo Stephen Owambo , Sircely Jason , Nijhof Ard M. , Bett Bernard 
Published: January 2025

Abstract
Crimean Congo hemorrhagic fever (CCHF) is a re-emerging tick-borne zoonosis that is caused by CCHF virus (CCHFV). The geographical distribution of the disease and factors that influence its occurrence are poorly known. We analysed historical records on its outbreaks in various countries across the sub-Saharan Africa (SSA) to identify hotspots and determine socioecological and demographicfactors associated with these outbreaks. We used data from historical outbreaks that were reported between 1981 and 2022 in various countries in SSA. To develop a common framework for merging the outbreak data and potential explanatory variables, we generated a common shapefile that combined Level 2 administrative units in all the countries. Several climatic, environmental, socioecological data were obtained from on-line GIS databases and extracted using the shapefile. The data were analysed using an approximate Bayesian hierarchical model using the R-INLA package. The outcome was a Boolean variable which indicated whether an administrative unit in the shapefile was affected in a given year or not. A neighborhood structure was also generated and used to account for spatial autocorrelation in the analysis. The final model that was obtained from the analysis was used to build a CCHF risk map. A total of 54 CCHF outbreaks were compiled across 414 districts in nine SSA countries. Factors that were positively associated with CCHF outbreaks included human population density, land area under grassland, bare soil cover and shrub cover. Conversely, high precipitation during wet months, elevated mean temperature and slope had negative effects. The risk map generated shows that CCHF occurrence risk is higher in arid and semi-arid land (ASAL) of West Africa, the Sahelian region, Central Africa, and the Eastern and Southern Africa region. The analysis identified ecological and demographic factors that are associated with CCHF outbreaks in SSA. This finding suggests the need to improve surveillance for the disease especially in the grasslands where the human population is increasing.
High-resolution investigations of fault architecture in space and time
Authors: Del Sole Leonardo , Viola Giulio , Aldega Luca , Moretto Vincenzo , Curzi Manuel , Xie Ruikai , Cantelli Luigi , Vignaroli Gianluca 
Published: January 2025

Abstract
Heterogeneous fault architecture affects crustal seismotectonics and fluid migration. When studying it, we commonly rely on static conceptual models that generally overlook the absolute time dimension of fault (re)activation. Heterogenous faults, however, represent the end-result of protracted, cumulative and intricate deformation histories. This may lead to inaccurate reconstructions of tectonic histories and flowed models of fault hydro-mechanical behavior. We adopt here a multitechnique approach building upon the examination of now juxtaposed but not coeval brittle structural facies (BSF), which offer multiscalar insights in the spatio-temporal-thermal fault evolution. Our approach is applied to the Carboneras Fault, unveiling a ~ 25 Myr-long polyphase structural and thermal evolution. This led to a complex fault architecture, where BSFs exhibit a stark heterogeneity in fault rock and permeability, ultimately generating very different space- and time-dependent fault hydro-mechanical behaviors. Therefore, fault architectures shall be seen as dynamic features from which to extrapolate time-integrated comprehensive fault models accounting for the entire deformed rock volume and fault life span. We demonstrate that high-resolution studies of fault architectures are required to elucidate modes of fault growth and evolution, decipher long-lived, polyphase tectonic and thermal histories, and understand the influence of heterogenous fault architecture on hydraulic compartmentalization and earthquake rupture dynamics.
How knee muscles and ground reaction forces shape knee buckling and ankle push-off in neuromuscular simulations of human walking
Authors: Buchmann Alexandra , Kiss Bernadett , Badri-Spröwitz Alexander , Renjewski Daniel 
Published: January 2025

Abstract
Ankle push-off is important for efficient, human-like walking, and many prosthetic devices mimic push-off using motors or elastic elements. The knee is extended throughout the stance phase and begins to buckle just before push-off, with timing being crucial. However, the exact mechanisms behind this buckling are still unclear. We use a predictive neuromuscular simulation to investigate whether active muscles are required for knee buckling and to what extent ground reaction forces (GRFs) drive it. In a systematic parameter search, we tested how long the knee muscles vastus (VAS), gastrocnemius (GAS), and hamstrings could be deactivated while maintaining a stable gait with impulsive push-off. VAS deactivation up to 35% of the gait cycle resulted in a dynamic gait with increased ankle peak power. GAS deactivation up to 20% of the gait cycle was detrimental to gait efficiency and showed reduced ankle peak power. At the start of knee buckling, the GRF vector is positioned near the knee joint’s neutral axis, assisting in knee flexion. However, this mechanism is likely not enough to drive knee flexion independently. Our findings contribute to the biomechanical understanding of ankle push-off, with applications in prosthetic and bipedal robotic design, and fundamental research on human gait mechanics.
Impact of electric vehicle battery recycling on reducing raw material demand and battery life-cycle carbon emissions in China
Authors: Jiang Rui , Wu Chengke , Feng Wei , You Kairui , Liu Jian , Zhou Guangmin , Liu Lujing , Cheng Hui-Ming 
Published: January 2025

Abstract
The rapid growth of electric vehicles (EVs) in China challenges raw material demand. This study evaluates the impact of recycling and reusing EV batteries on reducing material demand and carbon emissions. Integrating a national-level vehicle stock turnover model with life-cycle carbon emission assessment, we found that replacing nickel-cobalt-manganese batteries with lithium iron phosphate batteries with battery recycling can reduce lithium, cobalt, and nickel demand between 2021 and 2060 by up to 7.8 million tons (Mt) (67%), 12.4 Mt (96%), and 37.2 Mt (93%), respectively, significantly decreasing reliance on import. Moreover, battery recycling coupled with reuse can reduce carbon emissions by up to 6,532-6,864 Mt (36.0-37.9%), depending on four recycling methods employed. However, this reuse strategy delays battery recycling and risks lithium supply shortage, necessitating trade-offs between carbon reduction and material supply. Future technologies, such as lithium-sulfur and all-solid-state batteries, despite their energy efficiency, might exacerbate lithium shortage, underscoring the crucial need for increased lithium supply.
Analysis of electron spectra dynamics in a moving periodical ponderomotive potential
Authors: Kuchař Marek , Moriová Kamila , Kozák Martin 
Published: January 2025

Abstract
The interaction between freely propagating electrons and light waves is typically described using an approximation in which we assume that the electron’s velocity nearly does not change during the interaction. In this article we analytically describe the dynamics of electrons in an interaction potential generated by an optical beat wave beyond this regime and find a structure of sharp electron distribution peaks that periodically alternate in the energy/momentum spectrum. In classical description we analytically solve the nonlinear equation of motion, which is an analogy to mathematical pendulum. While addressing the problem using quantum mechanics we first use parabolic approximation of the interaction potential and then we also study the evolution of electron wavepacket in an infinite periodical potential. Using numerical simulations we show the classical and quantum evolution of the electron spectra during the interaction for different conditions and experimental settings.
Quantum dot distributed feedback laser grown on silicon with laterally coupled gratings
Authors: Yang Bo , Han Dong , Wei Wenqi , Cui Xiangru , Wang Zihao , Wang Ting , Zhang Jianjun 
Published: January 2025

Abstract
Direct epitaxy of quantum dot (QD) lasers on silicon is considered the holy grail of integrated silicon photonics. Various InAs/GaAs QD lasers grown directly on silicon substrates have been demonstrated but there has been limited research on single-longitudinal-mode lasers on silicon. Here, to avoid any regrowth procedures, distributed feedback (DFB) QD lasers on silicon are fabricated with lateral coupled (LC) gratings via a simplified fabrication process. The LC-DFB laser has a maximum laser power of 4.2 mW and threshold current of 80 mA under continuous-wave current mode at room temperature. Under an injection current of 110 mA, the side mode suppression ratio reaches 50 dB at room temperature. The relative intensity noise of the laser is measured as −135 dB Hz–1, with a corresponding optical linewidth of 3.5 MHz.
Multi-label segmentation of carpal bones in MRI using expansion transfer learning
Authors: Raith Stefan , Deitermann Matthias , Pankert Tobias , Li Jianzhang , Modabber Ali , Hölzle Frank , Hildebrand Frank , Eschweiler Jörg 
Published: January 2025

Abstract

Objective. The purpose of this study was to develop a robust deep learning approach trained with a small in-vivo MRI dataset for multi-label segmentation of all eight carpal bones for therapy planning and wrist dynamic analysis. Approach. A small dataset of 15 3.0-T MRI scans from five health subjects was employed within this study. The MRI data was variable with respect to the field of view (FOV), wide range of image intensity, and joint pose. A two-stage segmentation pipeline using modified 3D U-Net was proposed. In the first stage, a novel architecture, introduced as expansion transfer learning (ETL), cascades the use of a focused region of interest (ROI) cropped around ground truth for pretraining and a subsequent transfer by an expansion to the original FOV for a primary prediction. The bounding box around the ROI generated was utilized in the second stage for high-accuracy, labeled segmentations of eight carpal bones. Different metrics including dice similarity coefficient (DSC), average surface distance (ASD) and hausdorff distance (HD) were used to evaluate performance between proposed and four state-of-the-art approaches. Main results. With an average DSC of 87.8 %, an ASD of 0.46 mm, an average HD of 2.42 mm in all datasets (96.1 %, 0.16 mm, 1.38 mm in 12 datasets after exclusion criteria, respectively), the proposed approach showed an overall strongest performance than comparisons. Significance. To our best knowledge, this is the first CNN-based multi-label segmentation approach for MRI human carpal bones. The ETL introduced in this work improved the ability to localize a small ROI in a large FOV. Overall, the interplay of a two-stage approach and ETL culminated in convincingly accurate segmentation scores despite a very small amount of image data.
First-principles study of electronic and magnetic properties of self-intercalated van der Waals magnet Cr3Ge2Te6
Authors: Li Jia-wan , Zhao Shi-Bo , Zhuang Lin , Hou Yusheng 
Published: January 2025

Abstract
Self-intercalated van der Waals magnets, characterized by self-intercalating native atoms into van der Waals layered structures with intrinsic magnetism, exhibit a variety of novel physical properties. Here, using first-principles calculations and Monte Carlo simulations, we report a self-intercalated van der Waals ferromagnet, Cr3Ge2Te6, which has a high Curie temperature of 492 K. We find that Cr3Ge2Te6 is nearly half-metallic with a spin polarization reaching up to 90.9%. Due to the ferromagnetism and strong spin-orbit coupling effect in Cr3Ge2Te6, a large anomalous Hall conductivity of 138 Ω-1
cm
-1 and 305 Ω-1
cm
-1 can be realized when its magnetization is along its magnetic easy axis and hard axis, respectively. By doping electrons (holes) into Cr3Ge2Te6, these anomalous Hall conductivities can be increased up to 318 Ω-1
cm
-1 (648 Ω-1
cm
-1). Interestingly, a 5-layer Cr3Ge2Te6 thin film retains the room-temperature ferromagnetism with a higher spin polarization and larger anomalous Hall conductivity. Our work demonstrates that Cr3Ge2Te6 is a novel room-temperature self-intercalated ferromagnet with high spin polarization and large anomalous Hall conductivity, offering great opportunities for designing nano-scale electronic devices.
Measure-and-remeasure as an economically feasible approach to crediting soil organic carbon at scale
Authors: Potash Eric , Bradford Mark A , Oldfield Emily E , Guan Kaiyu 
Published: January 2025

Abstract
Agricultural carbon crediting predominantly relies on process-based biogeochemical models to estimate accrual of soil organic carbon stock (SOC). We investigate the conditions under which it may be economical to estimate SOC accrual by measuring and remeasuring SOC, which relies on fewer assumptions than modeling. We analyze multi-field measure-and-remeasure SOC projects with two key features: first, practice assignment is randomized to compare the effect of a treatment (e.g. no tillage) to a control (e.g. conventional tillage); second, a random subset of fields is sampled (two stage cluster sampling) to cost-effectively measure SOC changes. We use statistical modeling to characterize the estimated treatment effect, accounting for within-field and between-field variability in SOC change, as well as measurement error. We then use these statistics to evaluate how prices for measurement, treatment, and carbon credits influence the economics of measure-and-remeasure projects. We specifically investigate the potential advantages of larger spatial scale (number of fields) and temporal scale (years before remeasurement). We find economies of both spatial and temporal scale so that projects with thousands of fields, with only about 10% of fields measured for SOC change, are likely to yield a competitive return on investment in five years if the treatment effects found in the research literature can be achieved commercially. Our analysis suggests that measure-and-remeasure can be cost effective in both market and non-market SOC projects at scale. Moreover, measure-and-remeasure projects provide valuable data for independent validation on commercial farms of the accrual rates estimated by biogeochemical models using field trials. We provide next steps and software for researchers, credit registries, and project developers to move forward with measure-and-remeasure SOC projects.
Fundamental operating regimes, hyper-parameter fine-tuning and glassiness: towards an interpretable replica-theory for trained restricted Boltzmann machines
Authors: Fachechi Alberto , Agliari Elena , Aquaro Miriam , Coolen Anthony , Mulder Menno 
Published: January 2025

Abstract
We consider restricted Boltzmann machines with a binary visible layer and a Gaussian hidden layer trained by an unlabelled dataset composed of noisy realizations of a single ground pattern. We develop a statistical mechanics framework to describe the network generative capabilities, by exploiting the replica trick and assuming self-averaging of the underlying order parameters (i.e. replica symmetry). In particular, we outline the effective control parameters (e.g. the relative number of weights to be trained, the regularization parameter), whose tuning can yield qualitatively-different operative regimes. Further, we provide analytical and numerical evidence for the existence of a sub-region in the space of the hyperparameters where replica-symmetry breaking occurs.