bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of ultramarine blue in Roman wall paintings: case study from Volsinii (Bolsena, Italy)
Authors: Bernabale Martina , Felici Anna Candida , Atanasio Pierfrancesco , Buccini Luca , Passeri Daniele , Rossi Marco , Binaco Paolo , Dini Danilo 
Published: February 2025

Abstract
The identification of blue pigments in Roman wall paintings provides crucial insights into the materials, artistic techniques, and trade routes in the antiquity. The present study focuses on the analysis of a blue pigment lump discovered at Ponticello (Bolsena, Italy) initially thought to be Egyptian blue. The lump pigment is compared with two synthetic ultramarine pigments (Poggi and Divolo), “Herculaneum blue,” Egyptian blue, and natural lapis lazuli from Monte Somma, Italy. Through a multi-analytical approach that comprehends energy-dispersive X-ray fluorescence (ED-XRF) spectroscopy, micro-Raman spectroscopy, and X-ray powder diffraction (XRPD), the pigment was univocally identified as natural lazurite, the primary component of lapis lazuli. Chemometrics, including principal component analysis (PCA), was applied to the ED-XRF data to reveal patterns in the elemental composition of the samples. This finding is significant as ultramarine blue was a rare and expensive material in Roman times, which was traditionally sourced from distant regions like Afghanistan. While this study does not aim to determine the geographical provenance of the pigment, it offers important insights into Roman artistic practices, economic resources, and trade networks. Future research will explore the chemical composition of the pigments present in the frescoes from the archaeological area of Volsinii to provide important further insights into ancient material exchanges.

Graphical Abstract
GNOme, an ontology for glycan naming and subsumption
Authors: Zhang Wenjin , Vesser Michelle , Edwards Nathan 
Published: February 2025

Abstract
While GlyTouCan provides stable identifiers for referencing glycan structures, they are not organized semantically. GNOme, a glycan naming and subsumption ontology and a member of the OBOFoundry, organizes GlyTouCan accessions for automated reasoning and interactive browsing of glycan structures by subsumption. GNOme makes it quick and easy to discover glycans with a specific degree of characterization; provides a text-based table of common synonyms for specific structures and compositions; enumerates glycan subsumption relationships for automated reasoning; and assigns each glycan to well-defined categories based on their degree of characterization. As an OBOFoundry ontology, GNOme can be readily integrated with other OBOFoundry ontologies and standards initiatives that need to refer to glycans with various degrees of characterization. GNOme is integrated with GlyGen, a glycoinformatics knowledge base, providing navigation to “related glycans,” and expanding the utility of species and glycan classification annotations. GNOme is available at https://gnome.glyomics.org/ and via GlyGen, the OBO Foundry, and GitHub.

Graphical abstract
Effect of probenecid on the whole-body disposition of 6-bromo-7-[11C]methylpurine in humans assessed with long axial field-of-view PET/CT
Authors: Jackwerth Matthias , Mairinger Severin , Rausch Ivo , Weber Maria , Jorda Anselm , Nics Lukas , Langsteger Werner , Zeitlinger Markus , Hacker Marcus , Langer Oliver 
Published: February 2025

Abstract

Purpose
Multidrug resistance-associated proteins (MRPs) have a widespread tissue distribution. They play an important role in drug disposition and drug-drug interactions (DDIs) and have been associated with various diseases. PET with 6-bromo-7-[11C]methylpurine ([11C]BMP) has been used to assess MRP1 function in the brain and lungs of mice. [11C]BMP crosses cellular membranes by passive diffusion followed by intracellular conjugation with glutathione and MRP1-mediated efflux of the radiolabelled glutathione-conjugate. In this study, we assessed the effect of the prototypical organic anion transporter inhibitor probenecid on the whole-body disposition of [11C]BMP to examine its suitability for measuring the function of MRP1 and possibly other MRP subtypes across multiple tissues.

Methods
Seven healthy volunteers (3 women, 4 men) underwent two dynamic whole-body PET scans on a long axial field-of-view (LAFOV) PET/CT system after intravenous injection of [11C]BMP, without and with pre-treatment with a single oral dose of probenecid. Volumes of interest were outlined for several MRP-expressing tissues (cerebral cortex, cerebellum, choroid plexus, retina, lungs, myocardium, skeletal muscle, kidneys, and liver). Tissue time-activity curves were corrected for the contribution of vascular radioactivity and the elimination rate constant (k
E, h− 1) was calculated as a parameter for tissue MRP function.

Results
Radioactivity was primarily excreted into the urinary bladder and urinary clearance was significantly decreased after probenecid administration (− 50 ± 16%). Following probenecid administration, k
E was significantly decreased in the kidneys (− 43 ± 20%), liver (− 18 ± 15%), myocardium (− 16 ± 12%), skeletal muscle (− 51 ± 34%), and retina (− 57 ± 29%, non-blood-corrected).

Conclusion
Our study highlights the great potential of LAFOV PET/CT to assess drug disposition and transporter-mediated DDIs in humans at a whole-body, multi-tissue level. Due to the slow elimination of [11C]BMP-derived radioactivity from the human brain, [11C]BMP appears unsuitable to measure cerebral MRP1 function in humans, but it may be used to assess the function of MRP1 and possibly other MRP subtypes in various peripheral tissues.

Trial registration
EudraCT 2021-006348-29. Registered 15 December 2021.
Dynamic multi-period recycling collection routing with uncertain material quality
Authors: Cuellar-Usaquén Daniel , Ulmer Marlin W. , Antons Oliver , Arlinghaus Julia C. 
Published: February 2025

Abstract
We consider the problem of collecting and processing waste material. At a production facility, a known amount of inventory is required for production (e.g., paper) for every period. Instead of new material, the facility relies on collected and processed waste material (e.g., paper waste). This material is collected from regional waste collection locations. The amount of waste material per location is uncertain, as is the quality of the collected waste, i.e., the resulting inventory when processing the material. If the inventory is insufficient at the end of a period, costly new material must be bought. Each period, decisions are made about how much waste material to collect from which location and how to route the collection vehicles accordingly. Ideally, inventory is built to hedge against quality uncertainty and to ensure efficient routing operations in future periods. We propose a stochastic lookahead method that samples a set of scenarios and solves a simplified two-stage stochastic program in every period. We show the value of our method for two case studies, one based on real-world data from Sachsen-Anhalt, Germany, and one from the literature with data from the United Kingdom. We further conduct a detailed analysis of our method and the problem characteristics. The results show that our method effectively anticipates all sources of uncertainty, reducing cost significantly compared to benchmark policies. This superior performance is due to appropriate state-dependent supplier selection that considers the percentage of material loss, available material, and routing cost for current and future periods.
Environmental changes in central Mesoamerica in the Archaic and Formative periods
Authors: Caballero Margarita , Ortega Beatriz , Lozano-García Socorro , Montero Donají , Torres Esperanza , Soler Ana María 
Published: February 2025

Abstract
This study aims to improve the understanding of climatic fluctuations in the southern Basin of Mexico (BM) during the Archaic (11,500–4,000 cal bp) and Formative (4,000–2,000 cal bp) archaeological periods, when early sedentary settlements at the Zohapilco and Atlapulco sites developed from ∼8,000–7,500 cal bp. This study is based on the analysis of diatoms, pollen, microalgae, charcoal, magnetic susceptibility, geochemistry (organic carbon and titanium) and micromorphology in sediments from a section in a 5 m deep trench at Tulyehualco in the southern BM, close to the Zohapilco and Atlapulco archaeological sites. The chronology is based on five radiocarbon dates and on the correlation with two dated tephra layers. Abundant diatoms and microalgae attest for a period of high lake levels during the deglaciation (17,000–11,000 cal bp), followed by lowering lake levels during the Greenlandian (11,000–8,200 cal bp) when summer insolation peaked, and more oxidative subaerial conditions likely caused poor pollen preservation. Micromorphological analysis showed soil development processes and poor diatom and pollen preservation that confirmed subaerial (dry land) conditions during the 8,200 cal bp cold event. Zohapilco and Atlapulco were first occupied during this period of environmental difficulty. Better diatom and pollen preservation suggest a return to wetter conditions at ~ 7,500–6,500 cal bp, but unusually high charcoal concentrations could reflect human impact in the landscape since the mid Archaic. The diatom record showed that the late Formative (2,000 cal bp, 50 bc) abandonment of sites in the BM was associated with a new reduction in lake levels and a sedimentation hiatus.
Human-AI collaboration for ultrasound diagnosis of thyroid nodules: a clinical trial
Authors: Edström Axel Bukhave , Makouei Fatemeh , Wennervaldt Kasper , Lomholt Anne Fog , Kaltoft Mikkel , Melchiors Jacob , Hvilsom Gitte Bjørn , Bech Magne , Tolsgaard Martin , Todsen Tobias 
Published: February 2025

Abstract

Purpose
This clinical trial examined how the articifial intelligence (AI)-based diagnostics system S-Detect for Thyroid influences the ultrasound diagnostic work-up of thyroid ultrasound (US) performed by different US users in clinical practice and how different US users influences the diagnostic accuracy of S-Detect.

Methods
We conducted a clinical trial with 20 participants, including medical students, US novice physicians, and US experienced physicians. Five patients with thyroid nodules (one malignant and four benign) volunteered to undergo a thyroid US scan performed by all 20 participants using the same US systems with S-Detect installed. Participants performed a focused thyroid US on each patient case and made a nodule classification according to the European Thyroid Imaging Reporting And Data System (EU-TIRADS). They then performed a S-Detect analysis of the same nodule and were asked to re-evaluate their EU-TIRADS reporting. From the EU-TIRADS assessments by participants, we derived a biopsy recommendation outcome of whether fine needle aspiration biopsy (FNAB) was recommended.

Results
The mean diagnostic accuracy for S-Detect was 71.3% (range 40–100%) among all participants, with no significant difference between the groups (p = 0.31). The accuracy of our biopsy recommendation outcome was 69.8% before and 69.2% after AI for all participants (p = 0.75).

Conclusion
In this trial, we did not find S-Detect to improve the thyroid diagnostic work-up in clinical practice among novice and intermediate ultrasound operators. However, the operator had a substantial impact on the AI-generated ultrasound diagnosis, with a variation in diagnostic accuracy from 40 to 100%, despite the same patients and ultrasound machines being used in the trial.
MRI-guided laser interstitial thermal therapy in epilepsy: indications, technique and outcome in an adult population. A single-center data analysis
Authors: Infante Nazaret , Conesa Gerardo , Pérez-Enríquez Carmen , Capellades Jaume , de Oliveira Luísa Panadés , Vilella Laura , Principe Alessandro , del Mar Crespi-Vallespir Maria , Gallardo-Mir Mireia , Rocamora Rodrigo 
Published: February 2025

Abstract

Background
Magnetic Resonance Imaging guided Laser Interstitial Thermal Therapy (MRIgLITT) is a promising treatment for drug-resistant epilepsy (DRE) and an alternative to open surgery. However, the relationship between clinical and radiological factors and postoperative outcomes is unclear. This study explores the indications, technical challenges, and outcomes of MRIgLITT in terms of seizure control and cognitive changes across various pathologies.

Methods
A retrospective single-center analysis included 32 MRIgLITT procedures performed between January 2019 and December 2023. Procedures used the Visualase® system for laser ablation, with stereotactic robotic guidance for fiber placement. Data included demographics, clinical and surgical details (ablated volume, timing, power and accuracy), and postoperative follow-up assessed seizure outcomes and complications. Cognitive changes were analyzed using a Reliable Change Index (RCI) before and one year after the procedure.

Results
The 32 procedures involved 28 patients with MRI-diagnosed pathologies: 14 hippocampal sclerosis (HS), 7 hypothalamic hamartoma (HH), 3 focal cortical dysplasia (FCD), 2 periventricular heterotopia (PVH), 1 tuberous sclerosis complex (TSC), and 1 low-grade glioma. Some cases required multiple approaches.
Postoperative follow-up averaged 33 months. Among HS patients, 71.42% achieved Engel I, and 21.43% Engel II. In HH, 85.7% initially became gelastic seizure-free, with complete freedom after additional treatment. Engel I outcomes were 28.6%, while 57.2% showed significant improvement (Engel I + II). FCD patients had a 66.6% Engel I success rate. One PVH patient became seizure-free, while the TSC patient was Engel III at last follow-up. RCI analysis showed that 71.44% of patients experienced cognitive stability (RCI > −1.64) or improvement (RCI > 1.64) at one-year post-procedure.

Conclusions
MRIgLITT is a safe, minimally invasive alternative for epilepsy surgery, offering quicker recovery and showing better performance preserving cognitive function. It is particularly effective for deep or complex epileptic foci and patients who might refuse open surgery.
Intraspecific variation of the hedgehog arteriviruses, which may constitute a new genus in the subfamily Heroarterivirinae of the family Arteriviridae
Authors: Dastjerdi Akbar , Davies Hannah , Inglese Nadia , Holland Samantha , Samborskiy Dmitry V. , Gorbalenya Alexander E. 
Published: February 2025

Abstract
We recently discovered a novel member of the family Arteriviridae, hedgehog arterivirus 1 (HhAV-1), in the brains of hedgehogs with fatal encephalitis. In this study, we classified this virus and investigated its intrahost genomic diversity using next-generation sequencing. We sequenced HhAV-1 genomes from specimens from seven hedgehogs (two males and five females) with signs of encephalitis that were collected in Buckinghamshire, Gloucestershire, and Cambridgeshire, England, and had died or been euthanised between 2013 and 2024. Analysis of the intrahost populations of these seven HhAV-1 isolates and a previously described isolate revealed the presence of single-nucleotide polymorphisms (SNPs), which were most frequent in open reading frames 5, 6, and 7, encoding glycoprotein 5, the membrane protein, and the nucleocapsid protein. Pairwise comparisons of the eight HhAV-1 variants showed that the nucleotide sequence identity values in their combined complete coding sequences ranged from 76.2% to 100%. The eight HhAV-1 variants also shared at least 82.8% amino acid sequence identity in five domains that are involved in replication and are used for the classification of nidoviruses: 3CLpro, NiRAN, RdRp, ZBD, and HEL1. In a replicase-based phylogenetic tree of members of the family Arteriviridae, the HhAV-1 variants formed a sister cluster to African pouched rat arterivirus. A DEmARC-based pairwise distance analysis indicated that these viruses may comprise a new species, for which we propose the name "Xiarterivirus erinaceid", in a new genus in the subfamily Heroarterivirinae.
Clinical revenues of selective use of [18F]-FDG-PET/CT scanning in the management of Staphylococcus aureus bacteremia
Authors: Verkaik Dewi , Westgeest Annette C. , Wu Jian Ling , Sigaloff Kim C. E. , Lambregts Merel M. C. , de Boer Mark G. J. 
Published: February 2025

Abstract

Purpose
Although [18F]-FDG-PET/CT scanning (PET/CT) is recommended for managing Staphylococcus aureus bacteremia (SAB), its added value remains debated. This study investigated the clinical revenues of selective PET/CT use in SAB by considering three consequence-categories: detection of new infection foci, performance of new interventions, and alterations in antimicrobial therapy.

Methods
All adult patients with ≥ 1 blood culture (BC) positive with Staphylococcus aureus admitted in a Dutch academic center between 201711 and 202311 were identified. Standard practice was to order PET/CT for patients with community acquired SAB and/or positive BCs after ≥ 48 h of treatment, or if multiple foci, or persistent fever, or endocarditis were present. Clinical- and laboratory data were obtained from electronic health records. Numbers-needed-to-scan (NNT-scan) were calculated for each consequence-category. Regression analyses were performed to identify variables correlated with consequence-bearing PET/CT.

Results
Of 397 SAB patients, 143 (36%) underwent PET/CT. This led to detection of new foci in 73/143 patients (NNT-scan ≈ 2), new interventions in 33/143 patients (NNT-scan ≈ 4), and a change in antimicrobial therapy in 44/143 patients (NNT-scan ≈ 3). A CRP > 200 mg/L at presentation and positive follow-up BCs at 48 h were independently associated with interventions following PET/CT (adjusted OR and 95%CI 3.2 (1.2–8.3) and 2.6 (1.0-6.7) respectively). PET/CT results instigated changes in antimicrobial therapy predominantly in patients < 65 years and those with a CRP < 100 at presentation.

Conclusions
Selective PET/CT ordering in real-life practice resulted in a relatively low NNT-scan across all consequence-categories. Further research is warranted to optimize patient selection for PET/CT using clinical parameters or profiles.
Smallholder rice farmers' resilience to water insecurity in Ogun State Nigeria
Authors: Sanusi Muyinatu M. , Dries Liesbeth 
Published: February 2025

Abstract
Agriculture in Nigeria is essentially rainfed. This makes smallholder rice farming households vulnerable to water insecurity caused by weather-related shocks. This research assesses the resilience of smallholder rice farmers to water insecurity in Ogun State, Nigeria using cross-sectional data collected through an open data kit-powered questionnaire. The aim of the research is to examine the connection between specific resilience capacities of smallholder rice farming households and water insecurity caused by weather-related shocks. To this end, a measure of resilience to water insecurity is developed that incorporates household investments in water management techniques using a categorical principal component analysis. The potential correlation between the dimensions of resilience capacities and different types of weather-related shocks is tested. The research shows that smallholder rice farming households in the study area have a low overall level of resilience. Moreover, farmers are able to absorb shocks but their ability to adapt to shocks is low. It is therefore important to improve the capacities of farming households to become more structurally resilient to water insecurity in the long run by enhancing their ability to adapt, mitigate the impact of shocks, and implement coping strategies.
Online deep learning’s role in conquering the challenges of streaming data: a survey
Authors: Sulaiman Muhammad , Farmanbar Mina , Kagami Shingo , Belbachir Ahmed Nabil , Rong Chunming 
Published: February 2025

Abstract
In an era defined by the relentless influx of data from diverse sources, the ability to harness and extract valuable insights from streaming data has become paramount. The rapidly evolving realm of online learning techniques is tailored specifically for the unique challenges posed by streaming data. As the digital world continues to generate vast torrents of real-time data, understanding and effectively utilizing online learning approaches are pivotal for staying ahead in various domains. One of the primary goals of online learning is to continuously update the model with the most recent data trends while maintaining and improving the accuracy of previous trends. Based on the various types of feedback, online learning tasks can be divided into three categories: learning with full feedback, learning with limited feedback, and learning without feedback. This survey aims to identify and analyze the key challenges associated with online learning with full feedback, including concept drift, catastrophic forgetting, skewed learning, and network adaptation, while the other existing reviews mainly focus on a single challenge or two without considering other scenarios. This article also discusses the application and ethical implications of online learning. The results of this survey provide valuable insights for researchers and instructional designers seeking to create effective online learning experiences that incorporate full feedback while addressing the associated challenges. In the end, some conclusions, remarks, and future directions for the research community are provided based on the findings of this review.
Characterization of Delta-7 Alkenone Desaturase in Haptophyte Gephyrocapsa huxleyi Through Heterologous Expression in Tisochrysis lutea
Authors: Yoneda Kohei , Kobayashi Chinatsu , Araie Hiroya , Morita Rikuri , Harada Ryuhei , Shigeta Yasuteru , Endo Hirotoshi , Maeda Yoshiaki , Suzuki Iwane 
Published: February 2025

Abstract
The marine haptophyte Gephyrocapsa huxleyi is an ecologically and geochemically important phytoplankton due to its contribution to the global carbon cycle and its ability to biosynthesize certain alkenones. These alkenones are long-chain alkyl ketones with two to four trans-type double bonds. The genes encoding alkenone desaturase in G. huxleyi have not been experimentally characterized so far, partly due to the difficulty of inducing genetic transformation in G. huxleyi. Therefore, we introduced the putative alkenone delta-7 desaturase of G. huxleyi (designated “DesT”) to the transformable and alkenone-producing haptophyte Tisochrysis lutea. We found two types of coding sequences for DesT, which are probably derived from the expression products of different alleles, and designated them “DesT-1” and “DesT-2.” The ratio of C37:3 to C37:2 methyl alkenone in the DesT-1 transformant was significantly higher than that in the mock strain that expressed only the hygromycin resistance gene, suggesting that DesT-1 was an alkenone delta-7 desaturase in G. huxleyi. In the protein structure, a tunnel where a substrate alkenone penetrates was predicted to be located around the histidine box of DesT, and hydrophilic and hydrophobic amino acids were respectively located at the proximal (near side to the histidine box) and distal ends of the tunnel. This is the first study to conduct experimental characterization of the alkenone metabolism-related gene in G. huxleyi. The heterologous expression system using T. lutea paves the way for further characterization of the alkenone metabolism-related genes in less transformable haptophytes.
Kepler sets of linear recurrence sequences
Authors: Berend D. , Kumar R. 
Published: February 2025

Abstract
The Kepler set of a sequence

$$(a_n)_{n=0}^\infty$$

(

a
n

)

n
=
0

∞

is the closure of the set of consecutive ratios

$$\{a_{n+1}/a_{n} : n\geq 0\}$$

{

a

n
+
1

/

a
n

:
n
≥
0
}

. Following several studies, dealing with Kepler sets of recurrence sequences of order 2, we study here the case of recurrences of any order.