bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals
Authors: Vavoulis Dimitrios V. , Cutts Anthony , Thota Nishita , Brown Jordan , Sugar Robert , Rueda Antonio , Ardalan Arman , Howard Kieran , Matos Santo Flavia , Sannasiddappa Thippesh , Miller Bronwen , Ash Stephen , Liu Yibin , Song Chun-Xiao , Nicholson Brian D. , Dreau Helene , Tregidgo Carolyn , Schuh Anna 
Published: January 2025

AbstractThe analysis of circulating tumour DNA (ctDNA) through minimally invasive liquid biopsies is promising for early multi-cancer detection and monitoring minimal residual disease. Most existing methods focus on targeted deep sequencing, but few integrate multiple data modalities. Here, we develop a methodology for ctDNA detection using deep (80x) whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), a less destructive approach than bisulphite sequencing, which permits the simultaneous analysis of genomic and methylomic data. We conduct a diagnostic accuracy study across multiple cancer types in symptomatic patients, achieving 94.9% sensitivity and 88.8% specificity. Matched tumour biopsies are used for validation, not for guiding the analysis, imitating an early detection scenario. Furthermore, in silico validation demonstrates strong discrimination (86% AUC) at ctDNA fractions as low as 0.7%. Additionally, we successfully track tumour burden and ctDNA shedding from precancerous lesions post-treatment without requiring matched tumour biopsies. This pipeline is ready for further clinical evaluation to extend cancer screening and improve patient triage and monitoring.
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways
Authors: Müller Julian , Bayer Florian P. , Wilhelm Mathias , Schuh Maximilian G. , Kuster Bernhard , The Matthew 
Published: January 2025

AbstractPost-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform that offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams. PTMNavigator provides ~3000 canonical pathways from manually curated databases, enabling users to modify and create custom diagrams tailored to their data. Additionally, PTMNavigator automatically runs kinase and pathway enrichment algorithms whose results are directly integrated into the visualization. This offers a comprehensive view of the intricate relationship between PTMs and signaling pathways. We demonstrate the utility of PTMNavigator by applying it to two phosphoproteomics datasets, showing how it can enhance pathway enrichment analysis, visualize how drug treatments result in a discernable flow of PTM-driven signaling, and aid in proposing extensions to existing pathways. By enhancing our understanding of cellular signaling dynamics and facilitating the discovery of PTM-pathway interactions, PTMNavigator advances our knowledge of PTM biology and its implications in health and disease.
Structural basis of THC analog activity at the Cannabinoid 1 receptor
Authors: Thorsen Thor S. , Kulkarni Yashraj , Sykes David A. , Bøggild Andreas , Drace Taner , Hompluem Pattarin , Iliopoulos-Tsoutsouvas Christos , Nikas Spyros P. , Daver Henrik , Makriyannis Alexandros , Nissen Poul , Gajhede Michael , Veprintsev Dmitry B. , Boesen Thomas , Kastrup Jette S. , Gloriam David E. 
Published: January 2025

AbstractTetrahydrocannabinol (THC) is the principal psychoactive compound derived from the cannabis plant Cannabis sativa and approved for emetic conditions, appetite stimulation and sleep apnea relief. THC’s psychoactive actions are mediated primarily by the cannabinoid receptor CB1. Here, we determine the cryo-EM structure of HU210, a THC analog and widely used tool compound, bound to CB1 and its primary transducer, Gi1. We leverage this structure for docking and 1000 ns molecular dynamics simulations of THC and 10 structural analogs delineating their spatiotemporal interactions at the molecular level. Furthermore, we pharmacologically profile their recruitment of Gi and β-arrestins and reversibility of binding from an active complex. By combining detailed CB1 structural information with molecular models and signaling data we uncover the differential spatiotemporal interactions these ligands make to receptors governing potency, efficacy, bias and kinetics. This may help explain the actions of abused substances, advance fundamental receptor activation studies and design better medicines.
Charge-transfer complexation of coordination cages for enhanced photochromism and photocatalysis
Authors: Li Gen , Du Zelin , Wu Chao , Liu Yawei , Xu Yan , Lavendomme Roy , Liang Shihang , Gao En-Qing , Zhang Dawei 
Published: January 2025

AbstractIntensified host-guest electronic interplay within stable metal-organic cages (MOCs) presents great opportunities for applications in stimuli response and photocatalysis. Zr-MOCs represent a type of robust discrete hosts for such a design, but their host-guest chemistry in solution is hampered by the limited solubility. Here, by using pyridinium-derived cationic ligands with tetrakis(3,5-bis(trifluoromethyl)phenyl)borate (BArF−) as solubilizing counteranions, we report the preparation of soluble Zr-MOCs of different shapes (1-4) that are otherwise inaccessible through a conventional method. Enforced arrangement of the multiple electron-deficient pyridinium groups into one cage (1) leads to magnified positive electrostatic field and electron-accepting strength in favor of hosting electron-donating anions, including halides and tetraarylborates. The strong charge-transfer (CT) interactions activate guest-to-host photoinduced electron transfer (PET), leading to pronounced and regulable photochromisms. Both ground-state and radical structures of host and host-guest complexes have been unambiguously characterized by X-ray crystallography. The CT-enhanced PET also enables the use of 1 as an efficient photocatalyst for aerobic oxidation of tetraarylborates into biaryls and phenols. This work presents the solution assembly of soluble Zr-MOCs from cationic ligands with the assistance of solubilizing anions and highlights the great potential of harnessing host-guest CT for boosting PET-based functions and applications.
Investigating Parkinson’s disease risk across farming activities using data mining and large-scale administrative health data
Authors: Petit Pascal , Berger François , Bonneterre Vincent , Vuillerme Nicolas 
Published: January 2025

AbstractThe risk of Parkinson’s disease (PD) associated with farming has received considerable attention, in particular for pesticide exposure. However, data on PD risk associated with specific farming activities is lacking. We aimed to explore whether specific farming activities exhibited a higher risk of PD than others among the entire French farm manager (FM) population. A secondary analysis of real-world administrative insurance claim data and electronic health/medical records (TRACTOR project) was conducted to estimate PD risk for 26 farming activities using data mining. PD cases were identified through chronic disease declarations and antiparkinsonian drug claims. There were 8845 PD cases among 1,088,561 FMs. The highest-risk group included FMs engaged in pig farming, cattle farming, truck farming, fruit arboriculture, and crop farming, with mean hazard ratios (HRs) ranging from 1.22 to 1.67. The lowest-risk group included all activities involving horses and small animals, as well as gardening, landscaping and reforestation companies (mean HRs: 0.48–0.81). Our findings represent a preliminary work that suggests the potential involvement of occupational risk factors related to farming in PD onset and development. Future research focusing on farmers engaged in high-risk farming activities will allow to uncover potential occupational factors by better characterizing the farming exposome, which could improve PD surveillance among farmers.
An infrared, Raman, and X-ray database of battery interphase components
Authors: Karapin-Springorum Lukas , Sarycheva Asia , Dopilka Andrew , Cha Hyungyeon , Ihsan-Ul-Haq Muhammad , Larson Jonathan M. , Kostecki Robert 
Published: January 2025

AbstractFurther improvements to lithium-ion and emerging battery technologies can be enabled by an improved understanding of the chemistry and working mechanisms of interphases that form at electrochemically active battery interfaces. However, it is difficult to collect and interpret spectra of interphases for several reasons, including the presence of a variety of compounds. To address this challenge, we herein present a vibrational spectroscopy and X-ray diffraction data library of ten compounds that have been identified as interphase constituents in lithium-ion or emerging battery chemistries. The data library includes attenuated total reflectance Fourier transform infrared spectroscopy, Raman spectroscopy, and X-ray diffraction data, collected in inert atmospheres provided by custom sample chambers. The data library presented in this work (and online repository) simplifies access to reference data that is otherwise either diffusely spread throughout the literature or non-existent, and provides energy storage researchers streamlined access to vital interphase-relevant data that can accelerate battery research efforts.
Smart furniture using radar technology for cardiac health monitoring
Authors: Gharamohammadi Ali , Bagheri Mohammad Omid , Abu-Sardanah Serene , Riad Michael M. Y. R. , Abedi Hajar , Ansariyan Ahmad , Wang Kang , Saragadam Ashish , Chumachenko Dmytro , Abhari Shahabeddin , Morita Plinio Pelegrini , Khajepour Amir , Shaker George 
Published: January 2025

AbstractThe integration of radar technology into smart furniture represents a practical approach to health monitoring, circumventing the concerns regarding user convenience and privacy often encountered by conventional smart home systems. Radar technology’s inherent non-contact methodology, privacy-preserving features, adaptability to diverse environmental conditions, and high precision characteristics collectively establish it a compelling alternative for comprehensive health monitoring within domestic environments. In this paper, we introduce a millimeter (mm)-wave radar system positioned strategically behind a seat, featuring an algorithm capable of identifying unique cardiac waveform patterns for healthy subjects. These patterns are characterized by two peaks followed by a valley in each cycle, which can be correlated to Electrocardiogram (ECG), enabling effective cardiac waveform monitoring. The provided algorithm excels in discerning variations in heart patterns, particularly in individuals with prolonged corrected QT intervals, by minimizing high frequency breathing interference and ensuring accurate pattern recognition. Additionally, this paper addresses the influence of body movements in seated individuals, conducting a comprehensive study on heart rate variability and estimation. Experiment results demonstrate a maximum interbeat intervals (IBI) error of 30 milliseconds and an average relative error of 4.8% in heart rate estimation, showcasing the efficacy of the proposed method utilizing variational mode decomposition and a multi-bin approach.
Influence of ABCB1 polymorphisms on aripiprazole and dehydroaripiprazole plasma concentrations
Authors: Toja-Camba Francisco José , Vidal-Millares María , Durán-Maseda María José , Hermelo-Vidal Gonzalo , Carracedo Ángel , Maroñas Olalla , Ramudo-Cela Luis , Zarra-Ferro Irene , Fernández-Ferreiro Anxo , Mondelo-García Cristina 
Published: January 2025

AbstractAripiprazole (ARI) is an atypical antipsychotic which is a substrate of P-glycoprotein (P-gp), a transmembrane glycoprotein that plays a crucial role in eliminating potentially harmful compounds from the organism. ARI once-monthly (AOM) is a long-acting injectable form which improves treatment compliance. Genetic polymorphisms in ABCB1 may lead to changes in P-gp function, leading to individual differences in drug disposition. The present study aims to determine how the different variants of the three most prevalent SNPs of the ABCB1 gene affect plasma concentrations of ARI, of its active metabolite dehydroaripiprazole (DHA) and ARI/DHA ratio in patients under AOM treatment. The metabolizing state of the two main aripiprazole metabolizing enzymes (CYP2D6 and CYP3A4) were considered to specifically study the effect of P-gp on plasma concentrations of the parent compound and its active metabolite. The study found a clear relationship between the genotypes found for the different ABCB1 SNPs and the ARI/DHA ratio. Specifically, patients with GG genotype in G2677T have almost twice the ratio compared to TT genotype. Similarly, this increase is also found in C3435T with 1.4-fold and in C1236T with 1.6-fold for the same genotypes. Regarding haplotypes, significant differences were obtained between CC-GG-CC and TT-TT-TT patients, with an 87.9% higher ratio in patients with the CC-GG-CC haplotype. There was a clear trend towards lower ARI concentrations and higher DHA concentrations when the presence of mutated T alleles increases. The ABCB1 gene could be a good partner along with CYP2D6 and CYP3A4 genotyping in conjunction with monitoring ARI plasma concentrations.
Data-driven prediction of chemically relevant compositions in multi-component systems using tensor embeddings
Authors: Hayashi Hiroyuki , Tanaka Isao 
Published: January 2025

AbstractThe discovery of novel materials is crucial for developing new functional materials. This study introduces a predictive model designed to forecast complex multi-component oxide compositions, leveraging data derived from simpler pseudo-binary systems. By applying tensor decomposition and machine learning techniques, we transformed pseudo-binary oxide compositions from the Inorganic Crystal Structure Database (ICSD) into tensor representations, capturing key chemical trends such as oxidation states and periodic positions. Tucker decomposition was utilized to extract tensor embeddings, which were used to train a Random Forest classifier. The model successfully predicted the existence probabilities of pseudo-ternary and quaternary oxides, with 84% and 52% of ICSD-registered compositions, respectively, achieving high scores. Our approach highlights the potential of leveraging simpler oxide data to predict more complex compositions, suggesting broader applicability to other material systems such as sulfides and nitrides.
Facial signals shape predictions about the nature of upcoming conversational responses
Authors: Emmendorfer Alexandra K. , Holler Judith 
Published: January 2025

AbstractIncreasing evidence suggests that interlocutors use visual communicative signals to form predictions about unfolding utterances, but there is little data on the predictive potential of facial signals in conversation. In an online experiment with virtual agents, we examine whether facial signals produced by an addressee may allow speakers to anticipate the response to a question before it is given. Participants (n = 80) viewed videos of short conversation fragments between two virtual humans. Each fragment ended with the Questioner asking a question, followed by a pause during which the Responder looked either straight at the Questioner (baseline), or averted their gaze, or accompanied the straight gaze with one of the following facial signals: brow raise, brow frown, nose wrinkle, smile, squint, mouth corner pulled back (dimpler). Participants then indicated on a 6-point scale whether they expected a “yes” or “no” response. Analyses revealed that all signals received different ratings relative to the baseline: brow raises, dimplers, and smiles were associated with more positive responses, gaze aversions, brow frowns, nose wrinkles, and squints with more negative responses. Qur findings show that interlocutors may form strong associations between facial signals and upcoming responses to questions, highlighting their predictive potential in face-to-face conversation.
The role of worldviews, radicalization risk factors, and personality in harassment of scientists
Authors: Gligorić Vukašin , Reinhardt Carlotta , Nieuwenhuijzen Ella , de Castro Josha Orobio , Feddes Allard R. , van Kleef Gerben A. , Rutjens Bastiaan T. 
Published: January 2025

AbstractAnti-science movements brought more than public distrust in science. Perhaps even more worryingly, these movements are also associated with instances of harassment of—and violence against—scientists. However, virtually nothing is known about individuals likely to harass or harm scientists. Across two pre-registered studies (total N = 749), we investigated the role of worldviews (e.g., political ideology, conspiracy mentality, science cynicism), radicalization risk factors (relative deprivation and threat), and personality traits and how these relate to harassment of scientists (both attitudes and behavior). We found that science cynicism–the perception that scientists are incompetent and corrupt–drives approval of scientists’ harassment (attitudes), as well as harmful behavior (e.g., refusing to donate money, not signing a petition). Additionally, perceiving scientists as threatening, as well as dark personality traits (psychopathy and narcissism), contributed to approving scientists’ harassment. Overall, the present research takes a first step in identifying predictors of the willingness to harm scientists.
Advanced control parameter optimization in DC motors and liquid level systems
Authors: Ekinci Serdar , Izci Davut , Almomani Mohammad H. , Saleem Kashif , Zitar Raed Abu , Smerat Aseel , Snasel Vaclav , Ezugwu Absalom E. , Abualigah Laith 
Published: January 2025

AbstractIn recent times, there has been notable progress in control systems across various industrial domains, necessitating effective management of dynamic systems for optimal functionality. A crucial research focus has emerged in optimizing control parameters to augment controller performance. Among the plethora of optimization algorithms, the mountain gazelle optimizer (MGO) stands out for its capacity to emulate the agile movements and behavioral strategies observed in mountain gazelles. This paper introduces a novel approach employing MGO to optimize control parameters in both a DC motor and three-tank liquid level systems. The fine-tuning of proportional-integral-derivative (PID) controller parameters using MGO achieves remarkable results, including a rise time of 0.0478 s, zero overshoot, and a settling time of 0.0841 s for the DC motor system. Similarly, the liquid level system demonstrates improved control with a rise time of 11.0424 s and a settling time of 60.6037 s. Comparative assessments with competitive algorithms, such as the grey wolf optimizer and particle swarm optimization, reveal MGO’s superior performance. Furthermore, a new performance indicator, ZLG, is introduced to comprehensively evaluate control quality. The MGO-based approach consistently achieves lower ZLG values, showcasing its adaptability and robustness in dynamic system control and parameter optimization. By providing a dependable and efficient optimization methodology, this research contributes to advancing control systems, promoting stability, and enhancing efficiency across diverse industrial applications.
The trophic distribution of biomass in ecosystems with co-occurring wildlife and livestock
Authors: Speed James D. M. , Sobocinski Anna , Kolstad Anders L. , Linnell John D. C. , Solberg Erling J. , Mattisson Jenny , Austrheim Gunnar 
Published: January 2025

Abstract
Trophic interactions regulate populations, but anthropogenic processes influence primary productivity and consumption by both herbivore and carnivore species. Trophic ecology studies often focus on natural systems such as protected areas, even though livestock globally comprise the majority of terrestrial vertebrate biomass. Here we explore spatial and temporal patterns in the distribution of biomass between plants, and large herbivores and carnivores (> 10 kg) in Norwegian rangelands, including both wildlife and livestock. We find high spatial variation in the relationship between plant and herbivore biomass, with both positive and negative divergence in observed biomass from expectations based on primary productivity. Meanwhile, despite recent partial recoveries in carnivore densities across Norway, carnivore biomass is still lower than expected based on herbivore biomass, even if livestock are excluded from the estimation. Our study highlights how temporal trends in both herbivores and carnivores reflect policy development. The role of livestock husbandry and wildlife management is thus key in determining realised biomass distributions in anthropogenically influenced ecosystems.
Characterizing phenotype variants of Cercosporidium personatum, causal agent of peanut late leaf spot disease, their morphology, genetics and metabolites
Authors: Arias Renee S. , Cantonwine Emily G. , Orner Valerie A. , Walk Travis E. , Massa Alicia N. , Stewart Jane E. , Dobbs John T. , Manchester Atalya , Higbee Pirada S. , Lamb Marshall C. , Sobolev Victor S. 
Published: January 2025

AbstractCercosporidium personatum (CP) causes peanut late leaf spot (LLS) disease with 70% yield losses unless controlled by fungicides. CP grows slowly in culture, exhibiting variable phenotypes. To explain those variations, we analyzed the morphology, genomes, transcriptomes and chemical composition of three morphotypes, herein called RED, TAN, and BROWN. We characterized, for the first time in CP, anthraquinone (AQ) precursors of dothistromin (DOT), including averantin, averufin, norsolorinic acid, versicolorin B, versicolorin A, nidurufin and averufanin. BROWN had the highest AQ and melanin (15 mg/g DW) contents. RED had the highest ergosterol (855 µM FW) and chitin (beta-glucans, 4% DW) contents. RED and TAN had higher resistance to xenobiotics (p ≤ 1.0E-3), including chlorothalonil, tebuconazole and caffeine, compared to CP NRRL 64,463. In RED, TAN, and BROWN, rates of single nucleotide polymorphisms (SNP) (1.4–1.7 nt/kb) and amino acid changes (3k-4k) were higher than in NRRL 64,463. Differential gene expression (p ≤ 1.0E-5) was observed in 47 pathogenicity/virulence genes, 41 carbohydrate-active enzymes (CAZymes), and 23 pigment/mycotoxin biosynthesis genes. We describe the MAT1 locus, and a method to evaluate CP-xenobiotic resistance in 5 days. Chemical profiles indicate each CP morphotype could trigger different immune response in plants, probably hindering development of durable LLS resistance.