bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference Girls
Authors: Choi Jinhee 
Published: January 2025

Abstract
Drawing on the idea “reference image,” this chapter locates the “reference girl” of Korean cinema in the 1970s, whose image exposes the contradictory nature of the military government’s developmentalist ethos, an ethos that relies on girls’ labor yet expels their bodies. Regardless of their social positions, girls’ sexuality is repeatedly depicted as a commodity and their narrative fate is determined by their potential contribution to the economic development of the nation-state. The chapter examines the popular teen film cycle, the Really Really (jinjja jinjja) series, in particular the first and third installments, Never Forget Me (Moon Yeo-song, 1976) and Crazy for You (Moon Yeo-song, 1977), and their construction of male and female subjectivities in relation to their respective contribution to the modern nation-state. In addition to schoolgirls, who are most frequently tied to girlhood, it further examines girl protagonists with different social positions: a bus conductor in Girls from Scratch (1976) and a carefree girl in A Woman Like the Sun (1974), focusing on the girls’ viability as a potential labor force or lack thereof. The latter half of the chapter turns to Korean male veterans’ work: Yeong-ja’s Heydays (Kim Ho-sun, 1975), Insect Woman (Kim Ki-young, 1972), and Night Journey (a.k.a. Night Voyage, Kim Soo-yong, 1977)—how the girlhood glimpsed in each film underscores the social forces that constantly pull the female characters away from where they once belonged or hope to move forward.
Death of a Girl
Authors: Choi Jinhee 
Published: January 2025

Abstract
This chapter advances necro-cinematics by analyzing two comparable scenes from The Gangster, the Cop, the Devil (Lee Won-tae, 2019) and Memories of Murder (Bong Joon-ho, 2003); in both scenes, a girl is murdered to set up a male rivalry and/or create a moral dilemma for male characters. Through the comparative analysis of Mother (Bong Joon-ho, 2009), Poetry (Lee Chang-dong, 2010), and Han Gong-ju (Lee Sujin, 2013), all of which depict and trace a similar sexual crime, the chapter argues for the need of necro-cinematics: the deaths of Korean girl protagonists could result from both historical, colonial conditions (“necropolitics”) and the South Korean cinema’s narrative logic that exclude girls. Necro-cinematics would help to critically engage with the gender manifest in Bong’s girls films: The Host (2006), Snowpiercer (2013), and Okja (2017), which the Korean media unofficially name as a trilogy. Gender has rarely been at the center of the existing English-language scholarship on Bong, and necro-cinematics will help to show the girls’ fates rendered instrumentally within the South Korean and global film industry.
Accurate prediction of nucleic acid binding proteins using protein language model
Authors: Wu Siwen , Xu Jinbo , Guo Jun-tao 
Published: January 2025

Abstract

Motivation
Nucleic acid binding proteins (NABPs) play critical roles in various and essential biological processes. Many machine learning-based methods have been developed to predict different types of NABPs. However, most of these studies have limited applications in predicting the types of NABPs for any given protein with unknown functions, due to several factors such as dataset construction, prediction scope and features used for training and testing. In addition, single-stranded DNA binding proteins (DBP) (SSBs) have not been extensively investigated for identifying novel SSBs from proteins with unknown functions.

Results
To improve prediction accuracy of different types of NABPs for any given protein, we developed hierarchical and multi-class models with machine learning-based methods and a feature extracted from protein language model ESM2. Our results show that by combining the feature from ESM2 and machine learning methods, we can achieve high prediction accuracy up to 95% for each stage in the hierarchical approach, and 85% for overall prediction accuracy from the multi-class approach. More importantly, besides the much improved prediction of other types of NABPs, the models can be used to accurately predict single-stranded DBPs, which is underexplored.

Availability and implementation
The datasets and code can be found at https://figshare.com/projects/Prediction_of_nucleic_acid_binding_proteins_using_protein_language_model/211555.
VirDetector: a bioinformatic pipeline for virus surveillance using nanopore sequencing
Authors: Kaiser Nick Laurenz , Groschup Martin H , Sadeghi Balal 
Published: January 2025

Abstract

Summary
Virus surveillance programmes are designed to counter the growing threat of viral outbreaks to human health. Nanopore sequencing, in particular, has proven to be suitable for this purpose, as it is readily available and provides rapid results. However, as special bioinformatic programs are required to extract the relevant information from the sequencing data, applications are needed that allow users without extensive bioinformatics knowledge to carry out the relevant analysis steps. We present VirDetector, a bioinformatic pipeline for virus surveillance using nanopore sequencing. The pipeline automatically installs all required programs and databases and allows all its steps to be executed with a single console command. After preprocessing the samples, including the possibility for basecalling, the pipeline classifies each sample taxonomically and reconstructs the viral consensus genomes, which are then used in phylogenetic analyses. This streamlined workflow provides a user-friendly and efficient solution for monitoring viral pathogens.

Availability and implementation
VirDetector is freely available at https://github.com/NLKaiser/VirDetector and https://zenodo.org/records/14637302 (10.5281/zenodo.14637302).
Conceptual and ethical considerations in invasion science
Authors: Haubrock Phillip J , Parker Ben , Błońska Dagmara , Briski Elizabeta , Everts Teun , Fernandez Romina D , Kouba Antonín , Kourantidou Melina , Kurtul Irmak , Mammola Stefano , Musolin Dmitrii L , Nuñez Martin A , Olden Julian D , Rasmussen Jes J , Renault David , Russell James C , Sousa Ronaldo , Tarkan Ali Serhan , Britton J Robert 
Published: January 2025

Abstract
Invasion science addresses interconnected ecological, economic, and social challenges posed by the introduction of nonnative species. Therefore, invasion scientists have to consider and reconcile interdisciplinary needs while addressing the potential implications of their findings. Navigating diverse disciplines, including environmental sciences, ecology, economics, and the humanities, invasion scientists seek to arrive at informed decisions on invasion risk, impact, and management. Individual biases, uncertainties, and systemic pressures influence the ability to maintain objectivity and resist pressures that might otherwise distort their findings or applications. In the present commentary, we examine conceptual and ethical dilemmas within the field of invasion science, particularly reputational and the risks of the discipline perpetuating its own relevance by framing invasions as insurmountable challenges. In the discussion, we highlight how incentive structures, biased assessments and framing, and conflicts of interest may compromise the discipline's integrity. We also explore questions surrounding human responsibility to animal welfare and highlight ethical conundrums in the management of invasive species.
A systematic review of indocyanine green lymphography imaging for the diagnosis of primary lymphoedema
Authors: Brezgyte Greta , Mills Mike , van Zanten Malou , Gordon Kristiana , Mortimer Peter S , Ostergaard Pia 
Published: January 2025

Abstract

Objectives
This systematic review aims to evaluate the use of indocyanine green lymphography (ICGL) for the investigation of the lymphatics in the lower limbs of primary lymphoedema patients.

Methods
MEDLINE and EMBASE articles from January 1, 2000 to September 1, 2023 were searched for. A total of 11 studies were included in the review after a two-stage screening process.

Results
Data on patient demographics, ICG contrast injection technique, imaging protocols, and imaging outcomes were summarized and reviewed in detail. The review highlights the lack of commonality in protocols used. Factors important for good imaging are highly variable, particularly the number of injections, their location, and whether they are delivered intradermally or subcutaneously.

Conclusions
ICGL has strong potential to become a diagnostic tool to diagnose lymphoedema due to its non-ionizing nature and cost-effectiveness. However, due to the lack of thorough phenotyping and genotyping of patients included in the studies, uncertainty still exists as to the value of the described imaging features such as splash, starburst, and diffuse dermal rerouting patterns. Future studies, therefore, should aim to explore the diagnostic utility of ICGL for lymphoedema further through the imaging of primary lymphoedema patients with a confirmed genetic diagnosis and using standardized imaging protocols.

Advances in knowledge
ICGL is a strong candidate for advancing the diagnosis and understanding of primary lymphoedema, and monitoring response to treatment, but protocol heterogeneity and a lack of consistency in reporting imaging details and patient phenotyping currently hold it back.
Substantia nigra and locus coeruleus microstructural abnormalities in isolated rapid eye movement sleep behaviour disorder and Parkinson’s disease
Authors: Pasquini Jacopo , Firbank Michael J , Best Laura , Foster Victoria , Stewart Charlotte , Silani Vincenzo , Durcan Rory , Roberts Gemma , Petrides George , Ceravolo Roberto , Brooks David J , Anderson Kirstie N , Pavese Nicola 
Published: January 2025

Abstract
Substantia nigra (SN) and locus coeruleus (LC) are two catecholaminergic, neuromelanin-rich nuclei that are affected in Parkinson’s disease (PD) and may show neuroimaging abnormalities before the onset of motor manifestations. The simultaneous, multimodal investigation of their microstructural abnormalities may provide useful insights on the spatial diffusion and tissue characteristics of neurodegeneration, and this may in turn help develop markers for disease-modifying clinical trials. Therefore, through neuromelanin-sensitive and diffusion MRI, we aimed to investigate microstructural abnormalities in those nuclei in isolated REM sleep behaviour disorder (iRBD) and PD. Fourteen participants with polysomnography-confirmed iRBD, 18 with PD and 18 healthy controls were scanned with structural, neuromelanin-sensitive and neurite orientation dispersion and density imaging (NODDI) MRI. iRBD participants also underwent dopamine transporter imaging. SN neuromelanin and NODDI diffusion parameters and LC neuromelanin signals were extracted. Motor and global cognitive assessments were also collected. iRBD and PD participants showed significantly reduced neuromelanin contrast in the LC middle section compared with healthy controls. PD also showed significantly reduced caudal LC and posterior SN neuromelanin signal. No differences in SN NODDI parameters were detected between iRBD and healthy controls. Five iRBD participants showed reduced striatal dopamine transporter. In the combined disease groups (iRBD and PD), significant associations were shown between SN neuromelanin signal and neurite density index (r = −0.610, corr-p = 0.001) and between SN neurite density index and free water fraction (r = 0.417, corr-p = 0.042). In the same group, motor scores were negatively associated with nigral neuromelanin signal (r = −0.404, corr-p = 0.044) and free water fraction (r = 0.486, corr-p = 0.018). In conclusion, iRBD participants showed significant neuromelanin loss in the LC, with a minority showing initial nigrostriatal dopaminergic abnormalities. Across the entire iRBD–PD spectrum, the association between SN neuromelanin signal loss, diffusion parameters and motor scores has the potential to capture different yet related aspects of SN degeneration.
Fibroblast growth factor 23 and outcomes of atrial fibrillation: from clinical association to genetic evidence
Authors: Li Jiaju , Lai Yiwei , Jiang Chao , Li Mingxiao , Yang Zejun , Zhao Manlin , Peng Xiaodong , Li Sitong , Li Qifan , Chen Jiawei , Wang Zhen , Zhang Suhui , Ma Changsheng , Dong Jianzeng 
Published: January 2025

Abstract

Aims
Fibroblast growth factor 23 (FGF23) has been implicated in the occurrence of atrial fibrillation (AF), but its prognostic value in AF patients remains unclear.

Methods and results
A total of 35 197 AF patients with available follow-up data (3.56, 0.47–8.92 years) from the UK Biobank were included. Clinical association between serum FGF23 and AF-related outcomes including mortality, heart failure (HF), ischaemic stroke, and dementia were analysed using multivariable Cox regression. In those passed quality control for array sequencing, polygenic score for FGF23 (PGSFGF23) was calculated as genetic instrument, and the association between PGSFGF23 and the occurrence of endpoints after first AF diagnosis were further explored. In 886 patients who diagnosed AF at or prior to the enrolment, elevated serum FGF23 levels were significantly associated with an increased risk of all-cause (37% increase per standard deviation) and cardiovascular (40% increase per standard deviation) mortality and HF (43% increase per standard deviation). A total of 35 197 patients were available for genetic array sequencing data. Using polygenic score including seven independent SNPs reaching genome-wide significance threshold, genetic association analysis indicated that increased PGSFGF23 is associated with reduced risk of HF but increased risk of all-cause mortality and ischaemic stroke.

Conclusion
Our findings suggest that FGF23 is a potential biomarker for accessing AF-related outcomes. The paradoxical association between genetic FGF23 and serum FGF23 level highlights the need for further investigation to elucidate the underlying mechanisms.
Use of laser-ablation inductively-coupled plasma mass spectrometry for analysis of selenosugars bound to proteins
Authors: Bierla Katarzyna , Szpunar Joanna , Lobinski Ryszard , Sunde Roger A 
Published: January 2025

Abstract
We previously used high pressure liquid chromatography coupled with Se-specific inductively coupled plasma mass spectrometry and molecule specific (ESI Orbitrap MS/MS) detection to study the increase in liver Se in turkeys and rats supplemented as selenite in high-Se (5 µg Se/g diet) and adequate-Se diets. We found that far more Se is present as selenosugar (seleno-N-acetyl galactosamine) than is present as selenocysteine (Sec) in true selenoproteins. In high-Se liver, the increase in liver Se was due to low molecular weight selenometabolites such as glutathione-, cysteine-, and methyl-conjugates of the selenosugar, but also as high molecular weight species as selenosugars decorating general proteins via mixed Se-S bonds. To demonstrate selenosugar binding to proteins, aqueous liver extracts from animals fed Se-adequate and high-Se were subjected to sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and Native-PAGE with and without pretreatment with β-mercaptoethanol (βME). The separated proteins were then electrophoretically transferred to membranes, and the membranes subsequently were subjected to laser-ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) analysis of 78Se profiles. Without βME treatment, Se was widely distributed across the molecular weight profile for both SDS-PAGE and Native-PAGE, whereas βME pretreatment dramatically reduced Se binding, reducing the profile to true Sec-selenoproteins. This reduction was ∼50% for both high-Se rat and turkey extracts. The increased Se in non-βME treated samples was distributed across the full profile. The use of LA-ICP-MS indicates that selenosugar residues are bound to protein subunits of multiple sizes, and that targeted attachment of selenosugars to a single or limited number of protein subunits does not occur.
Dynamic photosynthetic labeling and carbon-positional mass spectrometry monitor in vivo RUBISCO carbon assimilation rates
Authors: Rajarathinam Yogeswari , Wittemeier Luisa , Gutekunst Kirstin , Hagemann Martin , Kopka Joachim 
Published: January 2025

Abstract
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) is the most abundant enzyme and CO2 bio-sequestration system on Earth. Its in vivo activity is usually determined by 14CO2 incorporation into 3-phosphoglycerate (3PGA). However, the radiometric analysis of 3PGA does not distinguish carbon positions. Hence, RUBISCO activity that fixes carbon into the 1-C position of 3PGA and Calvin–Benson–Bassham (CBB) cycle activities that redistribute carbon into its 2-C and 3-C positions are not resolved. This study aims to develop technology that differentiates between these activities. In source fragmentation of gas chromatography-mass spectrometry (GC-MS) enables paired isotopologue distribution analyses of fragmented substructures and the complete metabolite structure. GC-MS measurements after dynamic photosynthetic 13CO2 labeling allowed quantification of the 13C fractional enrichment (E13C) and molar carbon assimilation rates (A13C) at carbon position 1-C of 3PGA by combining E13C from carbon positions 2,3-C2 and 1,2,3-C3 with quantification of 3PGA concentrations. We validated the procedure using two GC-time of flight-MS instruments, operated at nominal or high mass resolution, and tested the expected 3PGA positional labeling by in vivo glycolysis of positional labeled glucose isotopomers. Mutant analysis of the highly divergent GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEs (GAPDH1 and 2) from Synechocystis sp. PCC 6803 revealed full inactivation of the CBB cycle with maintained RUBISCO activity in Δgapdh2 and a CBB cycle modulating role of GAPDH1 under fluctuating CO2 supply. RUBISCO activity in the CBB-deficient Δgapdh2 can re-assimilate CO2 released by catabolic pathways. We suggest that RUBISCO activity in Synechocystis can scavenge carbon lost through the pentose phosphate pathway or other cellular decarboxylation reactions.
Circulating secretory component-containing anti-citrullinated protein antibodies prior to symptom onset in rheumatoid arthritis
Authors: Martinsson Klara , Johansson Linda , Kastbom Alf , Rantapää-Dahlqvist Solbritt 
Published: January 2025

Abstract

Objectives
To investigate the occurrence and dynamics of secretory component-containing antibodies towards citrullinated proteins (SC ACPA) in plasma from pre-symptomatic individuals subsequently developing rheumatoid arthritis (RA).

Methods
We studied 319 individuals who had donated plasma prior to RA onset (median predating time 4.7 years), whereof 181 also donated samples after diagnosis. One hundred individuals were randomly selected from the same biobank cohorts to serve as controls. SC ACPA, total secretory IgA (TSIgA) and IgG ACPA were analysed in plasma by enzyme-linked immunoassays.

Results
Circulating SC ACPA levels in pre-symptomatic individuals and RA patients were significantly increased compared with controls [median (interquartile range) 108 (108), 179 (248) and 12.5 (537) AU/ml, respectively; P &lt; 0.001], and SC ACPA levels in RA patients were significantly increased compared with pre-symptomatic individuals (P &lt; 0.001). SC ACPA increased, in terms of both levels and proportion of positive samples, closer to symptom onset and diagnosis. TSIgA was not elevated compared with controls either during the pre-dating time or after diagnosis. The earliest detected SC ACPA positive sample was 9 years before symptom onset, as compared with 11 years for IgG ACPA. Only two pre-dating samples were positive for SC ACPA and negative for IgG ACPA.

Conclusions
Circulating SC ACPA responses arise and magnify during the asymptomatic phase of disease development in a subgroup of RA patients. This suggests mucosal involvement prior to both symptom onset and subsequent arthritis. As mirrored in the circulation, however, SC ACPA does not seem to precede the IgG ACPA response.
Regulatory trends of organophosphate and pyrethroid pesticides in cannabis and applications of the Comparative Toxicogenomics Database and Caenorhabditis elegans
Authors: Rivera Albert B , Stephens Ariell B , Conrow Kendra D , Griffith Symone T , Jameson Laura E , Cahill Thomas M , Sammi Shreesh R , Swinburne Mathew R , Cannon Jason R , Leung Maxwell C K 
Published: January 2025

Abstract
Organophosphate and pyrethroid pesticides are common contaminants in cannabis. Due to the status of cannabis as an illicit Schedule I substance at the federal level, there are no unified national guidelines in the United States to mitigate the health risk of pesticide exposure in cannabis. Here, we examined the change in the state-level regulations of organophosphate and pyrethroid pesticides in cannabis. The medians of pyrethroid and organophosphate pesticides specified by each state-level jurisdiction increased from zero pesticide in 2019 to 4.5 pyrethroid and 7 organophosphate pesticides in 2023, respectively. Next, we evaluated the potential connections between pyrethroids, organophosphates, cannabinoids, and Parkinson’s disease using the Comparative Toxicogenomics Database (CTD). Eleven pyrethroids, 30 organophosphates, and 14 cannabinoids were associated with 95 genes to form 3,237 inferred and curated Chemical-Gene-Phenotype-Disease tetramers. Using a behavioral repulsion assay with the whole organism model Caenorhabditis elegans, we examined the effect of cannabinoids and insecticides on depleting dopamine synthesis. Exposure to chlorpyrifos and permethrin, but not Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD), results in dose-dependent effects on 1-nonanol repulsive behaviors in C. elegans, indicating dopaminergic neurotoxicity (P &lt; 0.01). Dose-dependent effects of chlorpyrifos are different in the presence of Δ9-THC and CBD (P &lt; 0.001). As a proof of concept, this study demonstrated how to use new approach methodologies such as C. elegans and the CTD to inform further testing and pesticide regulations in cannabis by chemical class.