bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unfooling SHAP and SAGE: Knockoff Imputation for Shapley Values
Authors: Blesch Kristin , Wright Marvin N. , Watson David 
Published: October 2023

AbstractShapley values have achieved great popularity in explainable artificial intelligence. However, with standard sampling methods, resulting feature attributions are susceptible to adversarial attacks. This originates from target function evaluations at extrapolated data points, which are easily detectable and hence, enable models to behave accordingly. In this paper, we introduce a novel strategy for increased robustness against adversarial attacks of both local and global explanations: Knockoff imputed Shapley values. Our approach builds on the model-X knockoff methodology, which generates synthetic data that preserves statistical properties of the original samples. This enables researchers to flexibly choose an appropriate model to generate on-manifold data for the calculation of Shapley values upfront, instead of having to estimate a large number of conditional densities or make strong parametric assumptions. Through real and simulated data experiments, we demonstrate the effectiveness of knockoff imputation against adversarial attacks.
Open-Source System for Real-Time Functional Assessment of In Vitro Filtration Barriers
Authors: Fallon Tess K. , Zuvin Merve , Stern Alan D. , Anandakrishnan Nanditha , Daehn Ilse S. , Azeloglu Evren U. 
Published: October 2023

AbstractThe integrity of the barrier between blood and the selective filtrate of solutes is important for homeostasis and its disruption contributes to many diseases. Microphysiological systems that incorporate synthetic or natural membranes with human cells can mimic biological filtration barriers, such as the glomerular filtration barrier in the kidney, and they can readily be used to study cellular filtration processes as well as drug effects and interactions. We present an affordable, open-source platform for the real-time monitoring of functional filtration status in engineered microphysiological systems. Using readily available components, our assay can linearly detect real-time concentrations of two target molecules, FITC-labeled inulin and Texas Red-labeled human-serum albumin, within clinically relevant ranges, and it can be easily modified for different target molecules of varying sizes and tags. We demonstrate the platform’s ability to determine the concentration of our target molecules automatically and consistently. We show through an acellular context that the platform enables real-time tracking of size-dependent diffusion with minimal fluid volume loss and without manual extraction of media, making it suitable for continuous operational monitoring of filtration status in microphysiological system applications. The platform’s affordability and integrability with microphysiological systems make it ideal for many precision medicine applications, including evaluation of drug nephrotoxicity and other forms of drug discovery.
Interleukin-4 Modulates Neuroinflammation by Inducing Phenotypic Transformation of Microglia Following Subarachnoid Hemorrhage
Authors: Wang Jing , Wang Lili , Wu Qingjian , Cai Yichen , Cui Chengfu , Yang Ming , Sun Baoliang , Mao Leilei , Wang Yuan 
Published: October 2023

AbstractNeuroinflammation, a key pathological feature following subarachnoid hemorrhage (SAH), can be therapeutically targeted by inhibiting microglia M1 polarization and promoting phenotypic transformation to M2 microglia. Interleukin-4 (IL-4) is a pleiotropic cytokine known to its regulation of physiological functions of the central nervous system (CNS) and mediate neuroinflammatory processes. However, its specific role in neuroinflammation and microglia responses following SAH remains unexplored. In this investigation, we established both in vivo and in vitro SAH models and employed a comprehensive array of assessments, including ELISA, neurofunctional profiling, immunofluorescence staining, qRT-PCR, determination of phagocytic capacity, and RNA-Seq analyses. The findings demonstrate an elevated expression of IL-4 within cerebrospinal fluid (CSF) subsequent to SAH. Furthermore, exogenous administration of IL-4 ameliorates post-SAH neurofunctional deficits, attenuates cellular apoptosis, fosters M2 microglia phenotype conversion, and mitigates neuroinflammatory responses. The RNA-Seq analysis signifies that IL-4 governs the modulation of neuroinflammation in microglia within an in vitro SAH model through intricate cascades of signaling pathways, encompassing interactions between cytokines and cytokine receptors. These discoveries not only augment comprehension of the neuropathogenesis associated with post-SAH neuroinflammation but also present novel therapeutic targets for the management thereof.
Graphical Abstract
Effect of cooling rate during solidification on structure and mechanical properties of Cu45Zr48Al7 glass-forming alloy
Authors: Kozieł Tomasz , Cios Grzegorz , Rutkowski Bogdan , Wierzbicka-Miernik Anna , Pajor Krzysztof , Bała Piotr 
Published: October 2023

AbstractThe CuZr-based bulk metallic glass matrix composites have attracted great attention in recent years owing to their unique mechanical properties compared to bulk glassy samples. The vital effect of B2 CuZr phase on mechanical properties was previously confirmed in CuZr-based alloys with equiatomic concentrations of copper and zirconium. In this paper, the structures and mechanical properties of the Cu45Zr48Al7 alloy, which has hypereutectoid composition with respect to stoichiometric B2 CuZr phase, were studied. This alloy exhibits high glass-forming ability, but low tendency to form the B2 CuZr phase during solidification. However, we demonstrated that depending on the cooling rate during solidification, governed by sample diameter, either bulk metallic glass or bulk metallic glass matrix composite can be produced. In order to allow partial crystallization of the B2 phase during solidification with the volume fraction allowing to observe the strain hardening effect, the minimum cooling rate should be lower than 40 K/s. The composite consisting of a glassy outer layer and a crystalline core composed of the B2 phase exhibits fracture strength of the same level as the bulk glassy sample (above 1800 MPa) obvious work-hardening with a plastic deformation of about 6%.
Predictive Geochemical Exploration: Inferential Generation of Modern Geochemical Data, Anomaly Detection and Application to Northern Manitoba
Authors: Bourdeau Julie E. , Zhang Steven E. , Lawley Christopher J. M. , Parsa Mohammad , Nwaila Glen T. , Ghorbani Yousef 
Published: October 2023

AbstractGeochemical surveys contain an implicit data lifecycle or pipeline that consists of data generation (e.g., sampling and analysis), data management (e.g., quality assurance and control, curation, provisioning and stewardship) and data usage (e.g., mapping, modeling and hypothesis testing). The current integration of predictive analytics (e.g., artificial intelligence, machine learning, data modeling) into the geochemical survey data pipeline occurs almost entirely within the data usage stage. In this study, we predict elemental concentrations at the data generation stage and explore how predictive analytics can be integrated more thoroughly across the data lifecycle. Inferential data generation is used to modernize lake sediment geochemical data from northern Manitoba (Canada), with results and interpretations focused on elements that are included in the Canadian Critical Minerals list. The results are mapped, interpreted and used for downstream analysis through geochemical anomaly detection to locate further exploration targets. Our integration is novel because predictive modeling is integrated into the data generation and usage stages to increase the efficacy of geochemical surveys. The results further demonstrate how legacy geochemical data are a significant data asset that can be predictively modernized and used to support time-sensitive mineral exploration of critical minerals that were unanalyzed in original survey designs. In addition, this type of integration immediately creates the possibility of a new exploration framework, which we call predictive geochemical exploration. In effect, it eschews sequential, grid-based and fixed resolution sampling toward data-driven, multi-scale and more agile approaches. A key outcome is a natural categorization scheme of uncertainty associated with further survey or exploration targets, whether they are covered by existing training data in a spatial or multivariate sense or solely within the coverage of inferred secondary data. The uncertainty categorization creates an effective implementation pathway for future multi-scale exploration by focusing data generation activities to de-risk survey practices.
Country-scale assessment of urban areas, population, and households exposed to land subsidence using Sentinel-1 InSAR, and GPS time series
Authors: Fernández-Torres Enrique Antonio , Cabral-Cano Enrique , Solano-Rojas Darío , Salazar-Tlaczani Luis , Gárcia-Venegas Josue , Marquez-Azúa Bertha , Graham Shannon , Villarnobo-Gonzalez Katia Michelle 
Published: October 2023

AbstractThe increased need for water resources in urban sprawls and intense droughts has forced more aggressive groundwater extraction resulting in numerous urban areas undergoing land subsidence. In most cases, only some large metropolitan areas have been well-characterized for subsidence. However, there is no existing country-wide assessment of urban areas, population, and households exposed to this process. This research showcases a methodology to systematically evaluate urban localities with land subsidence higher than − 2.8 cm/year throughout Mexico. We used Interferometric Synthetic Aperture Radar (InSAR) tools with a dataset of 4611 scenes from European Space Agency’s Sentinel-1 A/B SAR sensors acquired from descending orbits from September 2018 through October 2019. This dataset was processed at a supercomputer using InSAR Scientific Computing Environment and the Miami InSAR Time Series software in Python software. The quality and calibration of the resulting velocity maps are assessed through a large-scale comparison with observations from 100 continuous GPS sites throughout Mexico. Our results show that an urban area of 3797 km2, 6.9 million households, and 17% of the total population in Mexico is exposed to subsidence velocities of faster than − 2.8 cm/year, in more than 853 urban localities within 29 land subsidence regions. We also confirm previous global potential estimations of subsidence occurrence in low relief areas over unconsolidated deposits and where groundwater aquifers are under stress. The presented research demonstrates the capabilities for surveying urban areas exposed to land subsidence at a country-scale level by combining Sentinel-1 velocities with spatial national census data.
Between harmonization and unification in the European higher education area: scenarios for the European university initiative
Authors: Kanniainen Jari-Pekka , Pekkola Elias 
Published: October 2023

AbstractThis article explores future scenarios regarding the integration of European higher education (HE) in light of the European Universities Initiative which has been unfolding since 2017. Its aim is to understand potential development paths in light of the established intergovernmental Bologna Process, which has been diversified through international and supranational practices since its launch at the end of the 1990s. By way of European integration theories, we approach potential integration scenarios – a hitherto underutilized framework in HE studies. Our heuristic analysis of HE integration is based on secondary data; subsequently we construct and discuss four scenarios. Finally, we explore the implications of the scenarios from the perspective of the evaluation of the integration process of European HE.
Germination performance of alien and native species could shape community assembly of temperate grasslands under different temperature scenarios
Authors: Trotta Giacomo , Vuerich Marco , Petrussa Elisa , Hay Fiona R. , Assolari Silvia , Boscutti Francesco 
Published: October 2023

AbstractRising temperatures due to climate change are expected to interplay with biological invasions, and may enhance the spread and growth of some alien species upon arrival in new areas. To successfully invade, a plant species needs to overcome multiple biological barriers. Among the crucial life stages, seed germination greatly contributes to the final species assembly of a plant community. Several studies have suggested that alien plant success is related to their high seed germination and longevity in the soil. Hence, our aim is to test if the germination potential of alien seeds present in the seed bank will be further enhanced by future warming in temperate dry grasslands, an ecosystem that is among those most prone to biological invasions. We designed a laboratory germination experiment at two temperatures (20 and 28 °C), to simulate an early or late heat wave in the growing season, using seeds from nine common grassland Asteraceae species, including native, archaeophyte and neophyte species. The test was performed on both single and mixed pools of these categories of species, using a full-factorial orthogonal design. The warmer germination temperature promoted neophyte success by increasing germination probability and germination speed, while negatively impacting these parameters in seeds of native species. The co-occurrence of native and archaeophyte seeds at the lower temperature limited the invasiveness of neophytes. These results provide important information on future management actions aimed at containing alien plant invasions, by improving our knowledge on the possible seed-bank response and interaction mechanisms of common species occurring in disturbed natural areas or restored sites.
Graphical abstract
Summary of the experimental results. The colour of the flowers represent the status, divided as native (blue), neophyte (red) and archaeophyte (green). Each flower symbol represents the species pool for each plant category (i.e. NA = Buphthalmum salicifolium, Carlina vulgaris, Centaurea scabiosa; NE = Artemisia annua, Symphyotrichum novi-belgii, Senecio inaequidens; AR = Centaurea cyanus, Cichorium intybus, Tripleurospermum inodorum). The number of flowers represent the germination percentage of the various category assembly. In the columns are divided the various combination. From up to bottom the trend of germination percentage at 20 and 28 °C are shown.
Genomic Mosaicism of the Brain: Origin, Impact, and Utility
Authors: Graham Jared H. , Schlachetzki Johannes C. M. , Yang Xiaoxu , Breuss Martin W. 
Published: October 2023

AbstractGenomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype—motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
A mixture distributions analysis based feature selection approach for bearing remaining useful life estimation
Authors: Huang Fei , Sava Alexandre , Adjallah Kondo H. , Zhang Dongyang 
Published: October 2023

AbstractFeature selection is a difficult but highly important preliminary step for bearings remaining useful life (RUL) estimation. To avoid the weights setting problem in hybrid metric, this work devotes to conduct feature selection by using a single metric. Due to noise and outliers, an existing feature selection metric, called monotonicity, used for estimating bearings RUL, requires data smoothing processing before adequate implementation. Such a smoothing process may remove significant part of meaningful information from data. To overcome this issue, a mixture distribution analysis-based feature selection metric is proposed. Moreover, based on this new metric, a feature selection approach for bearings RUL estimation is proposed. Numerical experiments benchmarking the proposed method and the existing metric monotonicity method on available real datasets highlight its effectiveness.
Spatially resolved CO2 carbon stable isotope analyses at the microscale using Raman spectroscopy
Authors: Remigi Samantha , Frezzotti Maria-Luce , Rizzo Andrea Luca , Esposito Rosario , Bodnar Robert J. , Sandoval-Velasquez Andres , Aiuppa Alessandro 
Published: October 2023

AbstractMeasuring the carbon stable isotope ratio (13C/12C, expressed as δ13CCO2) in geogenic CO2 fluids is a crucial geochemical tool for studying Earth's degassing. Carbon stable isotope analysis is traditionally performed by bulk mass spectrometry. Although Raman spectroscopy distinguishes 12CO2 and 13CO2 isotopologue bands in spectra, using this technique to determine CO2 isotopic signature has been challenging. Here, we report on in-situ non-destructive analyses of the C stable isotopic composition of CO2, applying a novel high-resolution Raman configuration on 42 high-density CO2 fluid inclusions in mantle rocks from the Lake Tana region (Ethiopia) and El Hierro (Canary Islands). We collected two sets of three spectra with different acquisition times at high spectral resolution in each fluid inclusion. Among the 84 sets of spectra, 58 were characterised by integrated 13CO2/12CO2 band area ratios with reproducibility better than 4‰. Our results demonstrate the determination of δ13CCO2 by Raman spectroscopy in individual fluid inclusions with an error better than 2.5 ‰, which satisfactorily matches bulk mass spectrometry analyses in the same rock samples, supporting the accuracy of the measurements. We thus show that Raman Spectroscopy can provide a fundamental methodology for non-destructive, site-specific, and spatially resolved carbon isotope labelling at the microscale.
Serum oxalate concentration is associated with coronary artery calcification and cardiovascular events in Japanese dialysis patients
Authors: Nishizawa Yoko , Miyata Satoshi , Tosaka Mai , Hirasawa Eriko , Hosoda Yumi , Horimoto Ai , Omae Kiyotsugu , Ito Kyoko , Nagano Nobuo , Hoshino Junichi , Ogawa Tetsuya 
Published: October 2023

AbstractCoronary artery calcification (CAC) is associated with cardiovascular disease (CVD). CAC might contain calcium oxalate, and a high serum oxalate (SOx) concentration is associated with cardiovascular mortality in dialysis patients. We assessed the associations between SOx and CAC or CVD events in Japanese hemodialysis patients. This cross-sectional and retrospective cohort study was done in 2011. Seventy-seven hemodialysis patients’ Agatston CAC score was measured, and serum samples were collected. SOx concentrations were measured in 2021 by using frozen samples. Also, new-onset CVD events in 2011–2021 were retrospectively recorded. The association between SOx concentration and CAC score ≥ 1000, and new-onset CVD events were examined. Median SOx concentration and CAC score were 266.9 (229.5–318.5) µmol/L and 912.5 (123.7–2944), respectively. CAC score ≥ 1000 was associated with SOx [adjusted odds ratio (OR) 1.01, 95% confidence interval (CI), 1.00–1.02]. The number of new-onset CVD events was significantly higher in patients with SOx ≥ median value [hazard ratio (HR) 2.71, 95% CI 1.26–6.16]. By Cox proportional hazard models, new-onset CVD events was associated with SOx ≥ median value (adjusted HR 2.10, 95% CI 0.90–4.91). SOx was associated with CAC score ≥ 1000 and new-onset CVD events in Japanese hemodialysis patients.
An underwater image enhancement model combining physical priors and residual network
Authors: Fan Xinnan , Zhou Xuan , Chen Hongzhu , Xin Yuanxue , Shi Pengfei 
Published: October 2023

AbstractDeep learning‐based methods have achieved notable performance for underwater image enhancement. However, previous studies are mostly focused on pursuing high similarity between the original image and the target, which incurs performance drop when the models are used for real‐world images. A new framework for underwater image enhancement is proposed to improve the generalization performance of enhancement. First, the coordinate attention module is integrated into the backbone network, which serves as a pre‐trained model, to strengthen the feature extraction capability of the network. Second, the backbone is finetuned by physical prior knowledge and real‐world images, in an unsupervised manner, to realize generalization from artificial images to real‐world images. Furthermore, a model protection mechanism is designed to guarantee the successful execution of the training. The experimental results indicate that the proposed method provides a powerful pre‐trained backbone network and the finetuning strategy can further solve the color distortion and improve the image sharpening, especially in the harsh real environment. Compared with relevant methods, the UCIQE and NIQE are, respectively, 0.525 and 4.149, with a 0.009–0.095 increase in UCIQE and a 0.256–1.032 decrease in NIQE compared to other methods.
Clinical assessment of upper limb impairments and functional capacity in Parkinson's disease: a systematic review
Authors: Capato Tamine T. C. , Rodrigues Rúbia , Cury Rubens G. , Teixeira Manoel Jacobsen , Barbosa Egberto R. 
Published: October 2023

Abstract
Background Parkinson's disease (PD) may progressively reduce the upper limb's functionality. Currently, there is no standardized upper limb functional capacity assessment in PD in the rehabilitation field.
Objective To identify specific outcome measurements to assess upper limbs in PD and access functional capacity.
Methods We systematically reviewed and analyzed the literature in English published from August/2012 to August/2022 according to PRISMA. The following keywords were used in our search: “upper limbs” OR “upper extremity” and “Parkinson's disease.” Two researchers searched independently, including studies accordingly to our inclusion and exclusion criteria. Registered at PROSPERO CRD42021254486.
Results We found 797 studies, and 50 were included in this review (n = 2.239 participants in H&Y stage 1–4). The most common upper limbs outcome measures found in the studies were: (i) UPDRS-III and MDS-UPDRS to assess the severity and progression of PD motor symptoms (tremor, bradykinesia, and rigidity) (ii) Nine Hole Peg Test and Purdue Pegboard Test to assess manual dexterity; (iii) Spiral test and Funnel test to provoke and assess freezing of upper limbs; (iv) Technology assessment such as wearables sensors, apps, and other device were also found.
Conclusion We found evidence to support upper limb impairments assessments in PD. However, there is still a large shortage of specific tests to assess the functional capacity of the upper limbs. The upper limbs' functional capacity is insufficiently investigated during the clinical and rehabilitation examination due to a lack of specific outcome measures to assess functionality.