bluuebunny/crossref_metadata_2025 huggingface dataset:
Single mode, distributed feedback interband cascade lasers grown on Si for gas sensing
Authors: Díaz-Thomas Daniel Andrés , Ayache Diba , Fagot Maëva , Loghmari Zeineb , Gilbert Audrey , Rouillard Yves , Baranov Alexei N. , Rodriguez Jean-Baptiste , Tournié Eric , Vicet Aurore , Cerutti Laurent
Published: January 2025

A single mode distributed feedback (DFB) interband cascade laser (ICL) grown on a (001) Si substrate has been developed. The designed DFB ICL with a grating on top of the ridge emits at a wavelength near 3.4 μm, suited for methane gas sensing, and operates in continuous wave up to 35 °C, with a maximum output power of 4 mW/facet at 15 °C and a side mode suppression ratio of 20 dB in the whole operating range. Methane detection has been demonstrated by integrating the DFB ICL on Si with a quartz-enhanced photoacoustic spectroscopy setup, a step forward in the development of integrated photonic gas sensors on silicon platforms.
Cryogenic cyclical etching of Si using CF4 plasma passivation steps: The role of CF radicals
Authors: Nos Jack , Iséni Sylvain , Kogelschatz Martin , Cunge Gilles , Lefaucheux Philippe , Dussart Rémi , Tillocher Thomas , Despiau-Pujo Émilie
Published: January 2025

Ultraviolet (UV) absorption spectroscopy is used to monitor the CF radical density in CF4 inductively coupled plasma (ICP) plasmas as a function of the substrate temperature. The CF density decreases dramatically when the wafer temperature is reduced from 20 to −130 °C by applying identical plasma conditions, demonstrating that the CF surface sticking coefficient increases as the surface temperature is reduced. This suggests that CF4 plasma could be used to form sidewall passivation layers and perform anisotropic etching at cryogenic temperature, which is impossible at room temperature. Subsequently, a cyclical Bosch type etching process of silicon was evaluated at −100 °C using CF4 plasma to passivate the trench sidewalls. Anisotropic etch profiles were obtained with an etch rate of 4.4 μm/min. Compared to a typical Bosch process using highly polymerizing c-C4F8 plasma, chamber wall contamination could be significantly reduced, alleviating a major issue of this cyclic process. Furthermore, CF4 has a 28% lower global warming potential than c-C4F8.
Kármán vortex street in a defective Bose–Einstein condensate
Authors: Xi Bao-Long , Shao Kai-Hua , Tu Pu , Xi Zhong-Hong , Zhao Xi , Su Rui-Ming , Ma Jin-Ping , Shi Yu-Ren
Published: January 2025

The wake evolution behind a moving impenetrable obstacle potential in a defective Bose–Einstein condensate (BEC) loaded in a shallow optical lattice is investigated. Exploiting the linear stability analysis method and potential flow theory, we analytically calculate the stability condition and velocity of Kármán vortex street, which agrees well with the numerical results. Based on it, the effects of defect on the stability of the Kármán vortex street and vortex pair shedding frequency are studied. The findings suggest that the stability of the vortex street deteriorates with the increase in lattice depth; however, special lattice constants can improve stability. It is worth noting that the shedding frequency of vortex pairs linearly increases with the obstacle velocity. Moreover, the relationship between critical velocity and vortex street structure parameters is established based on different expressions of shedding frequency, which may provide a new method for critical velocity measurement. Additionally, we also find that the Strouhal number (St) effectively characterizes the vortex street generation range when the impenetrable obstacle potential through BEC, which is significantly different from St≈0.21 in classical fluids.
The evolution of signaling and monitoring in plant–fungal networks
Authors: Scott Thomas W. , Kiers E. Toby , West Stuart A.
Published: January 2025

Experiments have shown that when one plant is attacked by a pathogen or herbivore, this can lead to other plants connected to the same mycorrhizal network up-regulating their defense mechanisms. It has been hypothesized that this represents signaling, with attacked plants producing a signal to warn other plants of impending harm. We examined the evolutionary plausibility of this and other hypotheses theoretically. We found that the evolution of plant signaling about an attack requires restrictive conditions, and so will rarely be evolutionarily stable. The problem is that signaling about an attack provides a benefit to competing neighbors, even if they are kin, and so reduces the relative fitness of signaling plants. Indeed, selection is often more likely to push plant behavior in the opposite direction—with plants signaling dishonestly about an attack that has not occurred, or suppressing a cue that they have been attacked. Instead, we show that there are two viable alternatives that could explain the empirical data: 1) the process of being attacked leads to a cue (information about the attack) which is too costly for the attacked plant to fully suppress; 2) mycorrhizal fungi monitor their host plants, detect when they are attacked, and then the fungi signal this information to warn other plants in their network. Our results suggest the empirical work that would be required to distinguish between these possibilities.
Male Separatism
Authors: Aiston Jessica
Published: January 2025

This book offers a critical discourse analytical perspective on the phenomenon of men who voluntarily abstain from relationships with women. Based on a case study of the online Reddit community known as ‘Men Going Their Own Way’, the author engages in qualitative examination of the argumentative and discursive strategies used to justify and legitimise an antifeminist, male separatist ideology. Methodologically, the book draws on the discourse-historical approach to critical discourse studies and investigates how members of this online community represent themselves, relationships with women, and the broader gendered social order. It considers male separatism as part of the new antifeminist social media network known as the manosphere, as well as part of a broader legacy of backlash against feminism and women’s rights. Overall, the book contributes to the growing body of literature on the manosphere and should be of interest to scholars in discourse studies, feminist media studies, and digital communication.
Achieving multi-unit turns
Authors: Afshari Saleh Reihaneh , Taleghani-Nikazm Carmen , Monfaredi Elham , Rezaee Parvaneh
Published: January 2025

This paper provides a conversation analytical and multimodal examination of a highly ubiquitous Persian token,
khob, in everyday Persian multi-unit tellings. Based upon corpora of daily interactions between family
members and friends over phone and face-to-face, three functions of khob are identified: (a)
khob can be used by the recipient to a telling as a response functioning as a continuer and acknowledgement
token, passing the opportunity for speakership, prompting the next unit of telling, and acknowledging the delivered prior turn. In
this function, khob can carry a rising or falling final pitch movement; (b) the token can also be used as a tag
by the speaker of a telling to elicit recipiency and check the recipient’s understanding of the turn so far. As a tag,
khob may or may not solicit a response. Response soliciting and non-soliciting khobs differ
in terms of the participants’ gaze behaviour and the coparticipants’ level of engagement in the storytelling, but both types only
appear with a final rise in our corpora. Finally, (c) khob can be used as a resumption marker, managing a return
to storytelling after it is suspended with an intervening action. Interactions were recorded in Iran.
Inhibition of DEK restores hematopoietic stem cell function in Fanconi anemia
Authors: Chen Zhe , Wu Feng , Li Yan , Li Lei , Lei Yufei , Gao Siwei , Chen Tao , Xie Yuxin , Xiao Jianwen , Zeng Hanqing , Deng Jianchuan , Zhao Xueya , Hou Yu
Published: January 2025

Hematopoietic stem cells (HSCs) are susceptible to replication stress, which is a major contributor to HSC defects in Fanconi anemia (FA). Here, we report that HSCs relax the global chromatin by downregulating the expression of a chromatin architectural protein, DEK, in response to replication stress. DEK is abnormally accumulated in bone marrow (BM) CD34+ cells from patients with FA and in Fancd2-deficient HSCs. DEK haploinsufficiency promotes chromatin relaxation, replication stress relief, and function recovery of Fancd2-deficient HSCs. Furthermore, inhibition of DEK restores the proliferation of FA CD34+ cells in vitro and enhances their engraftment in vivo. Mechanistically, the activating transcription factor 2 (ATF2), specifically phosphorylated ATF2 at Thr69/71, was identified as a promoter of DEK transcription. Fancd2 deficiency results in p38 hyperphosphorylation, which in turn phosphorylates ATF2 at Thr69/71, leading to DEK accumulation in HSCs. In conclusion, our findings establish a functional link between chromatin relaxation and replication stress tolerance in HSCs and highlight DEK as a target for FA.
Current-induced spin polarisation in Rashba–Dresselhaus systems under different point groups
Authors: Dey Akash , Nandy Ashis K , Saha Kush
Published: January 2025

Non-magnetic materials without inversion symmetry typically exhibit strong Rashba spin–orbit coupling (SOC), enabling the well-known Rashba Edelstein effect where an external electrical current induces transverse spin polarisation. In this study, we demonstrate that electrically induced spin polarisation in non-magnetic materials, for example, electronic systems within quantum-well geometries, can significantly be influenced by the system’s point-group symmetries, such as Cn
and C

nv
. These symmetries allow various linear and higher-order momentum,

k
−

varying SOC Hamiltonian. Specifically, we show that surfaces having C

n
point-group symmetry, which permits specific linear and cubic Rashba and Dresselhaus SOC terms, can lead to both orthogonal and non-orthogonal spin polarisations with respect to the applied field. In contrast, surfaces with C

nv
symmetry exhibit only transverse spin polarisation, regardless of the linear and cubic SOC terms. We further find contrasting spin polarisation for cubic-in-k SOC as compared to the linear-in-k SOC when energy is varied, for example, through doping. Additionally, we show that the surfaces with C

n
symmetry may exhibit persistent spin current, depending on the relative strength between different momentum-dependent SOC terms. Our finding emphasizes the significance of crystal symmetry in understanding and manipulating induced spin polarisation in noncentrosymmetric materials, especially in surface/interface systems.
Field-level simulation-based inference with galaxy catalogs: the impact of systematic effects
Authors: de Santi Natalí S.M. , Villaescusa-Navarro Francisco , Raul Abramo L. , Shao Helen , Perez Lucia A. , Castro Tiago , Ni Yueying , Lovell Christopher C. , Hernández-Martínez Elena , Marinacci Federico , Spergel David N. , Dolag Klaus , Hernquist Lars , Vogelsberger Mark
Published: January 2025

It has been recently shown that a powerful way to constrain cosmological parameters from galaxy redshift surveys is to train graph neural networks to perform field-level likelihood-free inference without imposing cuts on scale.
In particular, de Santi et al. [58] developed models that could accurately infer the value of Ωm from catalogs that only contain the positions and radial velocities of galaxies that are robust to different astrophysics and subgrid models.
However, observations are affected by many effects, including (1) masking, (2) uncertainties in peculiar velocities and radial distances, and (3) different galaxy population selections.
Moreover, observations only allow us to measure redshift, which entangles the galaxy radial positions and velocities. In this paper we train and test our models on galaxy catalogs, created from thousands of state-of-the-art hydrodynamic simulations run with different codes from the CAMELS project, that incorporate these observational effects.
We find that while such effects degrade the precision and accuracy of the models, the fraction of galaxy catalogs for which the models retain high performance and robustness is over 90%, demonstrating the potential for applying them to real data.
Stellar-mass black-hole binaries in LISA: characteristics and complementarity with current-generation interferometers
Authors: Buscicchio R. , Torrado J. , Caprini C. , Nardini G. , Karnesis N. , Pieroni M. , Sesana A.
Published: January 2025

Stellar-mass black-hole binaries are the most numerous gravitational-wave sources observed to date.
Their properties make them suitable for observation both by ground- and space-based detectors.
Starting from synthetic catalogues constructed based on
observational constraints from ground-based detectors, we
explore the detection rates and the characteristic parameters of the stellar-mass black-hole binaries observable by LISA during their inspiral, using signal-to-noise ratio thresholds as a detection criterion.
We find that only a handful of these sources will be detectable
with signal-to-noise ratio larger than 8:
about 5 sources on average in 4 years of mission duration, among which only one or two are multiband ones (i.e. merging in less than 15 years).
We find that detectable sources have chirp mass 10 M
⊙ ≲ ℳ
c
≲ 100 M
⊙, residual time-to-coalescence 4 yr ≲ τc
≲ 100 yr, and redshift z ≲ 0.1, much closer than those observed up to now by ground-based detectors.
We also explore correlations between the number of LISA detectable sources and the parameters of the population, suggesting that a joint measurement with the stochastic signal might be informative of the population characteristics.
By performing parameter estimation on a subset of sources from the catalogues, we conclude that, even if LISA measurements will not be directly informative on the population due to the low number of resolvable sources, it will characterise a few, low-redshift candidates with great precision.
Furthermore, we construct for the first time the LISA waterfall plot for low chirp-mass systems, as a function of their time to coalescence and inclination.
We demonstrate that LISA will also be able to
discriminate and characterize, through very precise parameter estimation, a population of binaries with higher masses, ℳ
c
∼ 𝒪(103) M
⊙, at the boundary of ground-based detectors sensitivity.
Bridging dark energy and black holes with EFT: frame transformation and gravitational wave speed
Authors: Mukohyama Shinji , Seraille Emeric , Takahashi Kazufumi , Yingcharoenrat Vicharit
Published: January 2025

Typically, constraints on parameters of the effective field theory (EFT) of dark energy have been obtained in the Jordan frame, where matter fields are minimally coupled to gravity. To connect these constraints with those of the EFT of black hole perturbations with a timelike scalar profile, it is necessary to perform a frame transformation on the EFT in general. In this paper, we study the conformal/disformal transformation of EFT parameters on an arbitrary background.
Furthermore, we explore the effect of an EFT operator M
6(r) σ̅

μ

ν

δK

ν

α

δK

α

μ
, which is elusive to the LIGO/Virgo bound on gravitational-wave speed, on the dynamics of odd-parity black hole perturbations. Intriguingly, a deviation from luminal propagation shows up only in the vicinity of the black hole, and the speeds of perturbations in the radial and angular directions are different in general due to the traceless part σ̅

μ

ν
of the background extrinsic curvature. This study establishes an important link between cosmological constraints and those obtained in the black hole regime.
Runaway electron beam formation, vertical motion, termination and wall loads in EU-DEMO
Authors: Vannini Francesco , Bandaru Vinodh Kumar , Bergström Hannes , Schwarz Nina , Artola F J , Hoelzl Matthias , Pautasso Gabriella , Nardon Eric , Maviglia Francesco , Richiusa M L , Emanuelli Enrico
Published: January 2025

Runaway electron loads onto material structures are a major concern for future large tokamaks due to the efficient avalanching at high plasma currents. Here, we perform predictive numerical studies using the JOREK code for a plausible plasma configuration in the European DEMO fusion power plant, focusing in this paper on the scenario where the highest multi-ampere runaway electron beam is formed.The work first comprises axisymmetric predictions of runaway electron beam formation in a mitigated scenario and of the simultaneous vertical motion of the beam due to loss of position control. The subsequent runaway electron beam termination triggered by a burst of MHD activity during the course of the vertical motion is then simulated in 3D with the runaway electron fluid self-consistently coupled to the MHD modes. Finally, the resulting deposition pattern of the runaway electrons onto wall structures is calculated with a relativistic test particle approach. This way, the suitability of a possible sacrificial limiter concept for the protection of first wall components is assessed.
Relaxation dynamics of integrable field theories after a global quantum quench
Authors: Salvo Emanuele Di , Schuricht Dirk
Published: January 2025

We apply the linked cluster expansion as well as the quench action approach to study the time evolution of one-point functions after a quantum quench in integrable field theories. We argue that the relaxation towards the stationary value fundamentally differs depending on the locality properties of the considered observable: while for local operators both exponential and power-law decaying terms are present in the dynamics, for semi-local operators the latter are absent. We explicitly confirm this for the Ising field theory, the sinh-Gordon model and the repulsive sine-Gordon model.
Improving tropical cyclone rapid intensification forecasts with satellite measurements of sea surface salinity and calibrated machine learning
Authors: Eusebi Ryan , Su Hui , Wu Longtao , Rong Pingping , Balaguru Karthik , Leung Ruby , Choi Yong-Sang , Chan Pak Wai , Gan Jianping , DeMaria Mark , Chirokova Galina
Published: January 2025

Forecasting rapid intensification (RI) of tropical cyclones (TC) is a mission known for large errors. One under-researched factor that affects TC intensification is salinity, which is important for density stratification in certain ocean regions and can affect the surface enthalpy flux under a strengthening hurricane. To investigate the impact and efficacy of using salinity information in state-of-the-art forecasting, we use a statistical model consisting of a variety of machine learning (ML) methods. For salinity data, we use satellite measurements of pre-storm sea surface salinity (SSS) as a proxy for the salinity stratification. We train and test the model on various ocean basins, including the Atlantic, eastern North Pacific and western North Pacific. A calibrator is trained on top of the ML models to correct and enhance probability forecasts. The calibrator significantly improves probability forecasts relative to recent works. The ML model performance is improved with the addition of SSS in the Eastern North Pacific, western North Pacific, and the Caribbean subregion of the North Atlantic, and the overall model performance is better than previous studies. SSS decreases model skill for a model trained on the full Atlantic basin. In the Indian Ocean, SSS is also notably correlated with RI occurrence, but the TC samples are not sufficient to train ML models.
Mangrove biomass productivity and sediment carbon storage assessment at selected sites in Mauritius: the effect of tidal inundation, forest age and mineral availability
Authors: Doodee M D D , Rughooputh S D D V , Jawaheer S
Published: January 2025

Carbon dioxide is the most abundant anthropogenic greenhouse gas released in the environment and is considered as one of the main drivers of global warming and ensuing climate change. Mangals, recognised as key ‘blue carbon’ ecosystems, are amongst the world’s most carbon-dense ecosystems and can sequester a considerable amount of carbon through biological carbon sequestration in their biomass and soils. In this work, five Rhizophora mucronata natural and planted forests in Mauritius were studied with the aims at evaluating the carbon storage potential and the effect of tidal inundation, forest age, and mineral availability on biomass productivity and sediment carbon storage. Using 25m x 25m quadrats and a simple random sampling technique, plant height and diameter at breast height (DBH) were measured in situ with the GLOBE Observer application (The Globe Program, NASA-sponsored) and a measuring tape, respectively. The rate of canopy coverage over the past twenty years was assessed using historical Landsat 7 and 8 images available on Google Earth Pro. Rhizophora allometric equations were used to estimate the above-ground biomass (AGB), below-ground biomass (BGB), and total biomass (TB). Total organic carbon (TOC), sediment carbon storage, and all essential nutrients for plant growth were analysed using standard methods. Soil texture was determined using granulometric analysis. Our findings show that in both natural and planted forests, the zones that were more inundated were first established. However, tree and sapling density, as well as biomass, were negatively correlated with sodium (density: r = −0.830; AGB: r = −0.880). Positive correlations between AGB and nitrate nitrogen (NO3-N) (r = 0.686), ammonium nitrogen (NH4-N) (r = 0.706), phosphate (r = 0.618), and manganese (r = 0.776) suggest that these minerals were limiting factors. Nevertheless, the combination of forest age and salinity was found to play key roles on the AGB and therefore on total organic carbon (TOC), which is linked to materials originating from the mangroves. High correlations of TOC with NH4-N (r = 0.822) and magnesium (r = 0.831) indicate the greater availability of these essential nutrients in older forests. It is noteworthy that the Ferney forest with a relatively lower salinity (5–15 ppt) and the only forest that had already reached a steady state in 2010, had a relatively much higher AGB (326.2 ± 26.3 t ha−1) than the global average for Rhizophora mucronata (94.8 t ha−1), let alone Rhizophora spp. (281 t ha−1). The TOC registered at Ferney (47.34%) was also higher than the global values reported (2.00 ± 2.20% to 40.00 ± 2.20%).
Deep mining of megawatt large wind turbine actual operating data: exploration of Bayesian parameter fusion modeling
Authors: Wu Weimin , Liu Xiongfei , Ren Yu , Zhang Suocheng , Yan Wanjun , Du Wenqiang
Published: January 2025

Real-time operation data analysis and condition monitoring of large wind turbines are crucial for efficient and safe operation of wind farms. In response to this, an accurate prediction model architecture based on the multivariate linear regression algorithm is proposed for a deeper understanding of the actual operation of large wind turbines. Comparing different prediction variables, we have confirmed that the average wind direction and average wind speed play a core role in predicting active power. The display has significantly better approximation than the traditional multiple linear regression (MLR), especially in the peak region of period-like variation. The quasi-periodic peak variation characteristics of the active power near the observed series 2000, 2500 and 3000 are realized, and the peak prediction results of B-MLR are significantly better than those of traditional MLR. Meanwhile, for RMSE and R-squared, B-MLR is significantly better than the traditional MLR algorithm in the active power prediction of wind turbines. However, the data complexity in actual applications poses a challenge to the effectiveness of the Bayesian fusion algorithm. Further optimization of the algorithm is needed to cope with the complex and variable real data environment. This study provides scientific evidence for the efficient operation, precise maintenance, and environmentally friendly design of wind turbines, promoting the continuous progress and development of wind power generation technology.
Bridging theory and practice in peer-to-peer energy trading: market mechanisms and technological innovations
Authors: Raghoo Pravesh , Shah Kalim
Published: January 2025

The article provides a synthesis of the literature on the peer-to-peer (P2P) energy trading paradigm. P2P energy trading is a prosumer business model and a transformative concept that allows prosumers to sell surplus generation to other prosumers and consumers within an energy community or microgrid. P2P energy trading is a novel concept to promote decentralization, decarbonization, democratization, digitalization, and enhancing energy resilience of the energy sector. The article covers different facets of P2P energy trading, including market designs, changing actor roles, pricing mechanisms, enabling technologies, and challenges. The article thus addresses emerging and complementary aspects not covered in prior literature reviews. As such, three market designs are discussed: centralized, decentralized, and distributed, and four pricing mechanisms, which are optimization, game theory, auction-based, and reinforcement learning. Enabling technologies discussed are Energy Internet, Internet of Things, Artificial intelligence, Blockchain, Communication networks, and battery flexibility. The paper discusses the challenges that the development and commercialization of the P2P energy trading faces—especially focusing on the social ontology of the concept—and provides research directions to amplify the scaling up of the technology.
Learning Citizenship Matters
Authors: Shanahan Brendan A
Published: January 2025

This chapter examines the proliferation of state anti-alien professional licensure laws and hiring policies during the early to mid-twentieth century and explores legal, political, and administrative battles over their implementation. Unlike concurrent blue-collar nativist hiring measures, anti-alien professional licensure laws rarely became “dead letters” in practice when unemployment was low. Instead, state licensing board members, who generally had little expertise in immigration and citizenship law, frequently adopted harsh ad hoc documentation requirements and applied them unsparingly when East and South Asian immigrants, women, and refugees sought licensure. Immigrant professionals and their allies fiercely resisted these laws before judges and licensing board members. They also appealed to voters and policymakers for aid. But their efforts found limited success prior to the early Cold War. This chapter argues that the growing ubiquity and tortuous enforcement of nativist state licensure laws increasingly concretized citizenship rights as citizen-only rights in American professional employment.
Reference Girls
Authors: Choi Jinhee
Published: January 2025

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

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

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

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

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

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

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.
Introduction to the hydrogen industry special issue
Authors: Zheng Jinyang
Published: January 2025

This special issue highlights the generation, application, and safe use of low-carbon hydrogen produced from renewable energy sources.
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

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

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

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

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 < 0.001], and SC ACPA levels in RA patients were significantly increased compared with pre-symptomatic individuals (P < 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.