bluuebunny/crossref_metadata_2025 huggingface dataset:
Unlocking the advantage of qubit communication in multi-node network configurations
Authors: Chakraborty Ananya , Gopalkrishna Naik Sahil , Lobo Edwin Peter , Patra Ram Krishna , Sen Samrat , Alimuddin Mir , Mukherjee Amit , Banik Manik
Published: February 2025

The extension of point-to-point communication to multi-node configurations has significant applications in internet and telecommunication networks. Quantum resources promise notable advantages in such settings. Here, we demonstrate a novel quantum advantage in simulating multiple access channels (MACs)-a common network configuration where multiple distant senders transmit messages to a single receiver (e.g. the uplink from several mobile phones to a server). Specifically, we show that qubit transmission outperforms its classical counterpart, even when the latter is supplemented with classical shared randomness. Remarkably, unlike the seminal quantum superdense coding protocol, this advantage is achieved without any pre-shared entanglement between the senders and the receiver-a feat prohibited by Holevo and Frenkel–Weiner no-go theorems in the one-sender-one-receiver scenario. The receiver’s ability to simultaneously decode quantum systems from multiple senders underpins this distinct advantage in the MAC setup. Some of our MAC designs are inspired by constructs in quantum foundations, such as the Pusey–Barrett–Rudolph theorem and ‘quantum nonlocality without entanglement’. Beyond network applications, this quantum advantage reveals a deeper connection to ‘quantum nonlocality without inputs’ phenomenon and suggests potential for semi-device-independent certification of entangled measurements.
Impact of weld pool geometry on the welding temperature field of 50mm thick Q460-GJ steel plates
Authors: Sun Xuejun , Mao Congbing , Fu Yanqing , Cui Haixin , Ma Guangzhe
Published: February 2025

This article utilizes finite element software to calculate and analyze the impact of the molten pool geometry on the welding temperature field during the multi-layer and multi-pass welding process of Q460-GJ steel plates. Addressing the issue of how the molten pool shape affects the peak temperature and temperature distribution of each weld pass during welding, a finite element simulation was conducted for a thick plate with seven layers and 22 weld passes using numerical simulation. By adjusting the size of the double-ellipsoidal heat source model, finite element results considering the impact of the molten pool geometry were obtained. The results show that in the model without considering the molten pool geometry, the temperature of each weld pass ranges from 900°C to 2400°C, with 85% of the area having a temperature higher than 1500°C. In contrast, in the model considering the molten pool geometry, the temperature of each weld pass ranges from 2000°C to 2200°C, with 100% of the area having a temperature higher than 1500°C. The results considering the molten pool geometry are more consistent with the actual conditions.
On the crystallography of plastic flow instabilities in FCC metals during impact loading: a study modelled on copper single crystals
Authors: Paul Henryk , Puchlerska Sandra , Mania Izabela
Published: February 2025

The formation of shear bands (SBs) at high strain rates directly precedes the fracture of metals. Their appearance in the microstructure signals a reduction or complete loss of the load-bearing properties of a metallic parts. This paper analyses the crystallographic aspects of the mechanism responsible for the occurrence of this form of unstable metal flow under model conditions. The study examined Cu single crystals with unstable orientations close to C{112}<111> and S{123}<634>, which were deformed to logarithmic strains of 0.9 in a channel-die, with the punch driven by explosive energy to achieve a strain rate of 4 × 105 s−1. Microstructure and texture evolutions were characterized across a wide range of scales, primarily using scanning and transmission electron microscopy techniques. In both orientations analysed, the extremely high strain rate leads to intense deformation twinning, on all four {111} planes. The appearance of compact twin bundles of two generation, directly precedes the formation of SB. In each of the analysed cases, the rigid-body rotation of the crystal lattice in the band region, along with twinning in the reoriented matrix platelets, increases the density of texture components around the G{110}<001> orientation.
Synthesis and characterization of novel 5-substituted indanones via Suzuki coupling reactions
Authors: Ökten Salih , Derin Yavuz , Yilmaz Raşit Fikret , Tutar Ahmet
Published: February 2025

1-Indanone and its derivatives are well known for their diverse biological activities, making them valuable scaffolds in drug design and medicinal chemistry. Among the various synthetic methodologies available for modifying such structures, the Suzuki-Miyaura cross-coupling reaction is a prominent approach for constructing carbon-carbon bonds. In this study, the palladium-catalyzed Suzuki-Miyaura cross-coupling reaction of 5-bromo-1-indanone with four different boronic acids—phenylboronic acid, 4-methoxyphenylboronic acid, 4-thiomethylphenylboronic acid, and 4-ethylphenylboronic acid—was investigated. The reactions yielded the corresponding 5-substituted indanone derivatives, which were characterized by 1H and 13C NMR spectroscopy to confirm their structures and assess their purity. This study demonstrates the efficiency and versatility of the Suzuki-Miyaura reaction in functionalizing 1-indanone derivatives, providing a robust route for synthesizing structurally diverse compounds with potential applications in medicinal chemistry. The newly synthesized and characterized 5-indanone derivatives have potential applications in the development of new drug candidates. These compounds may contribute to advancements in treatments for various diseases, including cancer and Alzheimer’s disease, by integrating into biologically active structures.
Investigate the aluminium 1050-H4 microstructure, hardness, and wear characteristics when reinforced with maize cob particles
Authors: Pita M. , Lebea L.
Published: February 2025

One of the effects of creating composite materials, which are classified as advanced materials, is a change to their mechanical properties. In this study, the effect of reinforcing aluminium 1050-H4 using corn-cob particles were investigated. Prior to being examined using scanning electron microscopy (SEM), the corn cob was crushed and milled in the experiment using a Aimil machine. The hardness, microstructure and wear behavior test were carried out. The aluminium alloy reinforced with corn cob particles of two distinct diameters, <0.425 mm and 0.425 mm, to create the composites. Casted samples were characterized by scanning Electron microscope (SEM). The findings indicate that adding maize cob particles larger than 0.425 mm in diameter improves the mechanical characteristics (hardness) of the aluminium matrix composite by 6.9% and raises its coefficient of friction and wear rate.
Alternative cosmologies
Authors: López-Corredoira Martín
Published: February 2025

A few remarkable examples of alternative cosmological theories are shown, ranging from a compilation of variations on the Standard Model (inhomogeneous universe, Cold Big Bang, varying physical constants or gravity law, zero-active mass, Milne cosmology, cyclical models), through the more distant quasi-steady-state cosmology, plasma cosmology, or universe models as a hypersphere such as the Dynamic Universe, to the most exotic cases including static models with non-cosmological redshifts of galaxies.

Most cosmologists do not usually work within the framework of alternative cosmologies very different from the standard one because they feel that these are not at present as competitive as the standard model. It is true that they are not so developed, but that is because cosmologists do not work on them. This vicious circle is to a great extent due to a sociological phenomenon known as the “snowball effect”, in which resources are distributed to the most successful theory at a given time; the effect acts as a potential in a field that attracts cosmologists, causing funds, research positions, prestige, telescope time, publication in top journals, citations, conferences, and other resources to be dedicated almost exclusively to standard cosmology.
On the Motivations for Seeking a Theory of Quantum Gravity
Authors: Crowther Karen
Published: February 2025

While there are some empirical problems that could suggest the need for a theory of quantum gravity, most of these are not standardly taken as motivations for seeking a new theory. Rather, the quest for a theory of quantum gravity has been primarily motivated, guided, and constrained by philosophical and theoretical concerns. A critical examination of these can help us better understand what the theory is supposed to achieve—and, further, what it should be expected to achieve. On the other hand, there are various approaches towards finding a theory of quantum gravity, with different aims, methods, and starting-points—they disagree on what the theory is supposed to be like. A relevant question is then: what is it that unites these approaches such that we classify them as approaches to quantum gravity? This paper argues that a basic characterisation of the theory can be given in terms of the minimal shared motivation across these different approaches, and that this itself can be seen as motivated by various other problems that have been appealed to as reasons for seeking a theory of quantum gravity.
The Dynamic Universe
Authors: Suntola Tuomo
Published: February 2025

We are accustomed to thinking that the relativity of observations results from variations in time and distance, as taught by the theory of relativity. This theory is built on kinematics and metrics. Historically, this observer-centered approach was natural due to the lack of a deeper understanding of physics and space. The Dynamic Universe theory offers a different perspective. It incorporates our current understanding of space and the physics underlying atomic processes. In this framework, relativity can be understood as a direct consequence of the conservation of total energy and the connection between the local and the whole. DU uses time and distance as universal coordinate quantities, essential for human comprehension. DU describes space as a spherically closed entity, specifically a 3-dimensional surface of a 4-dimensional sphere (often called a “3-sphere” in mathematics). In this model, the energies of gravitation and motion are in balance, which links the speed of light and the rest energy of matter to the expansion of space. As a result, the locally available rest energy and the rate of physical processes become functions of the state of motion and gravitation. DU offers a framework that unifies relativity and quantum phenomena. It provides precise predictions for observations ranging from microsystems to cosmology, along with a comprehensible picture of the universe as a whole.
Beyond wave-particle dualism: How Suntola’s mass-wave concept unites physics and metaphysics
Authors: Kallio-Tamminen Tarja
Published: February 2025

The article evaluates the significance of Tuomo Suntola’s Dynamic Universe (DU) theory from physical, metaphysical, and cultural perspectives. It demonstrates how Suntola’s concept of the mass wave, derived by removing the speed of light from Planck’s constant, resolves the wave-particle dualism, enabling a better understanding of quantum phenomena and the nature of reality. Within DU, the Newtonian mechanical and deterministic clockwork world is replaced by a dynamic and self-organizing entity that develops completely according to law, but not deterministically. This unified formalism encompasses phenomena dealt with by relativity theory, cosmology, and quantum physics, providing a comprehensive world-view where events can be described objectively in an immutable 4-dimensional coordinate system. Such a scientific revolution, replacing abstract and unintuitive standard theories with an entire world-view, allows for a deeper understanding of reality and our place within it. The restoration of a comprehensible overall map could improve the quality of human performance in both environmental matters and personal lives.
Infrared measurements of the JWST suggest that our dynamic universe is spatially closed
Authors: Křížek Michal
Published: February 2025

Global geometry and shape of the physical universe may be revealed by observing objects at large cosmological redshift z, since for small z the universe seems almost flat. Recent infrared measurements of the James Webb Space Telescope (JWST) indicate that there exist very luminous galaxies at distances z ≥ 13 that should not exist according to the standard ΛCDM cosmological model for the flat universe with curvature index k = 0. We introduce a spacetime-lens principle that could explain why these very distant galaxies shine so much. We show that the observed large flux luminosities may be mere optical effects due to the positive curvature index k = 1 of an expanding 3-sphere modeling our physical universe in time. For Euclidean or hyperbolic geometries such large flux luminosities seem implausible. This suggests that the right model of a homogeneous and isotropic physical universe for each fixed time instant is a 3-sphere. The standard cosmological model is based on the normalized Friedmann equation ΩM + ΩΛ + Ω
k
= 1, where ΩM + ΩΛ = 1 by measurements. We also show that this does not imply that Ω
k
= 0 and k = 0 as it is often claimed.
Was David Bohm a Wave Function Realist?
Authors: Pylkkänen Paavo
Published: February 2025

One of the more radical ideas to have emerged in recent metaphysics of quantum theory is wave function realism, according to which the fundamental spatial framework of the world is one of very many dimensions. At first sight this idea sounds similar to the notion of a multidimensional implicate order the physicist David Bohm proposed on the basis of quantum theory in the 1980s. This paper briefly considers Bohm’s various attempts to provide a realist interpretation of the wave function in order to clarify whether or not Bohm was anticipating and even endorsing wave function realism with his implicate order theory. The underlying question is what quantum theory — and non-locality in particular — is trying to tell us about the more fundamental nature of the physical world.
Can physics and neuroscience allow for free will?
Authors: Liljenström Hans
Published: February 2025

While most of us feel we make decisions and can act out of free will, science seems to say we cannot. Neither deterministic laws of nature, acting in our macroscopic world, nor indeterministic quantum processes at microscopic levels, appear to allow for any free will. In addition, psychophysical experiments of voluntary actions by Libet and others seem to indicate that the brain decides our actions up to seconds before we are aware that we make a decision to act. All of these reasons have been taken as arguments for free will being an illusion. Here, I will discuss some of the perceived problems with free will, and how alternative interpretations of theories and experiments may lead to a different conclusion regarding the existence of free will. I will also argue that contemporary physics is insufficient for dealing with the behavior of complex biological systems, and in particular consciousness and agency. I conclude that, in order to allow for consciousness and free will, science needs to be extended beyond chance and necessity, which currently are the only models of explanation science can provide.
Examining future changes in coastal low-level jet properties offshore California through dynamical downscaling
Authors: Juliano Timothy W , McGinnis Seth , Bukovsky Melissa S , Liu Ye , Brummet Thomas , Ellen Haupt Sue , Krishnamurthy Raghavendra
Published: February 2025

The coastal low-level jet, or coastal low-level jet (CLLJ), is a synoptically-forced meteorological feature frequently present offshore the western United States (U.S.). Characterized by a wind speed maximum that resides at the top of the marine boundary layer, the CLLJ is largely controlled by the location and strength of the North Pacific High (NPH) as well as the coastal geometry. Considering the rich wind resource available in this offshore region, the Bureau of Ocean Energy Management identified wind energy lease areas offshore California and supported the deployment of two U.S. Department of Energy wind lidar buoys near Morro Bay and Humboldt. Despite our relatively good understanding of the fundamental mechanisms responsible for large-scale CLLJ properties offshore the western U.S., future changes in CLLJ characteristics are less clear. To address this research challenge, and ultimately to better inform future wind turbine deployments, we use simulations driven by three global climate models (GCMs). We apply self-organizing maps to the model outputs for a historical and two future climate periods to show the range of NPH regimes that support CLLJ conditions during the warm seasons, as well as the subtle contribution from land-falling cyclones approaching the mainland during the cold seasons. Compared to the historical period, the three GCM-driven simulations agree that CLLJ conditions will become more (less) prevalent from central California northward (southward). They agree less with respect to future changes in maximum CLLJ wind speeds and CLLJ heights. However, after considering model biases present during the historical period, wind speeds between the models are actually more similar during the 2070–2095 period than during the historical period. The potential combination of more frequent CLLJ conditions characterized by relatively consistent wind speeds occurring at lower heights across northern California suggests that the Humboldt lease area may be ideal for a long-term wind turbine deployment.
Study of attenuation characteristics for novel neonatal head phantom in diagnostic radiology using Monte Carlo simulations and experiments
Authors: Sekkat Hamza , Abdellah Khallouqi , El Rhazouani Omar , Madkouri Youssef , Halimi Abdellah
Published: February 2025

This study presents the design and validation of a neonatal head phantom using innovative heterogeneous composite materials customized to replicate the x-ray attenuation properties of neonatal cranial structures. Analysis of Hounsfield Unit (HU) data from 338 neonatal head CT scans informed the design of epoxy resin-based composites with additives such as sodium bicarbonate, fumed silica, and acetone to simulate bone, brain matter, cerebrospinal fluid (CSF) and hyperdense abnormalities. The cranial bone substitute (60% epoxy resin, 40% sodium bicarbonate) achieved a density of 1.60 g cm−3, with HU values (574.67–608.04) closely matching clinical ranges. Brain matter (95% epoxy resin, 5% acetone) achieved HU values (35.27–43.61), aligning with clinical means, while the CSF-equivalent material (80% epoxy resin, 15% fumed silica, 5% acetone) matched neonatal CSF HU values (14.53–17.02). A mass substitute for hyperdense abnormalities exhibited HU values (56.16–61.07), enabling differentiation from normal brain. Validation included Monte Carlo simulations and experimental CT imaging, showing close agreement in linear attenuation coefficients, with deviations below 11% across energy levels. Mass attenuation coefficients from simulations and XCOM software were consistent, with deviations under 0.7%, confirming the materials dosimetric reliability. The phantom, with a cylindrical geometry (9 cm diameter, 10 cm length), provides accurate attenuation properties across 80–120 kVp energy levels, with deviations below 5% between experimental CT numbers and simulation data. This phantom offers a robust platform for neonatal imaging research, enabling impactful dose optimization and imaging protocol adjustment and supports improved diagnostic accuracy in pediatric imaging.
Afterlives of coal: land and transition dynamics in Central Appalachia
Authors: Shade Lindsay , Schwartzman Gabe , Rignall Karen , Slovinsky Kevin , Johnson Jacob
Published: February 2025

The US has witnessed unprecedented federal investments targeted to “energy communities” since 2021. Scholars, policy-makers, and activists have long sought to promote policies that ensure that energy transitions bring about just outcomes. However, emerging political frameworks for decarbonization and energy source transition frequently neglect to account for the role of incumbent actors in upholding long standing legal, economic, and political arrangements that produce uneven distributions of benefits and burdens in energy systems. In this paper, we reflect on ongoing energy transition efforts in Central Appalachia, sharing our experiences from community-based research documenting the localized effects of carbon forestry offsets, solar energy projects, and postmine land uses, such as prisons, that are structurally linked to concentrated land ownership and capture of federal investments by legacy actors who have long dominated local and regional extraction regimes. We argue that the success or failure of broad-based transition policies depends largely on place-based dynamics rooted in land: who controls the land, who has access to land, who benefits from investments in land, and how public revenues flow from land. Empirical analysis of the politics of land from the local vantage point offers insights into how elites who have historically controlled the extractive economy continue to shape the landscape, but also opens up different worlds of possibilities that emerge at different scales.
Criteria for smoothness of positroid varieties via pattern avoidance, Johnson graphs, and spirographs
Authors: Billey Sara , Weaver Jordan
Published: February 2025

Positroids are certain representable matroids originally studied by Postnikov in connection with the totally nonnegative Grassmannian and now used widely in algebraic combinatorics. The positroids give rise to determinantal equations defining positroid varieties as subvarieties of the Grassmannian variety. Rietsch, Knutson-Lam-Speyer, and Pawlowski studied geometric and cohomological properties of these varieties. In this paper, we continue the study of the geometric properties of positroid varieties by establishing several equivalent conditions characterizing smooth positroid varieties using a variation of pattern avoidance defined on decorated permutations, which are in bijection with positroids. This allows us to give two formulas for counting the number of smooth positroids along with two

q
q

-analogs. We include enumerative results due to Christian Krattenthaler which follow from these formulas. Furthermore, we give a combinatorial method for determining the dimension of the tangent space of a positroid variety at key points using an induced subgraph of the Johnson graph. We also give a Bruhat interval characterization of positroids.
New Voices of the Countryside
Authors: Ribi Forclaz Amalia
Published: February 2025

Chapter 5 examines how from the mid-1930s onwards, the ILO’s work on agriculture began to change in tone and outreach, mostly as a result of new international currents. Due to the mutual reinforcement of the economic crisis and growing political mobilization, new political movements stepped into the fray, from women’s organizations to fascist and leftist ones, targeting rural populations, rural issues, and agricultural policies. At the same time, non-European experts increasingly challenged the ILO’s narrow focus on European waged farm labour, pointing to the large number of poor subsistence farmers that did not fall under the Organization’s remit. Ongoing problems about the way in which agricultural labour was being recruited in the colonies and about forms of indentured labour that resembled servitude also came to the fore, changing the tone and geographical orientation of the debate.
Conclusion
Authors: Ribi Forclaz Amalia
Published: February 2025

The Conclusion draws together the main themes of the book. It reviews some of the achievements and shortcomings of the ILO’s work on agriculture between the 1920s and the 1950s and traces how post-war industrialization and agrarian modernization influenced the ILO’s work. It also reflects on the continuing challenge of improving the labour conditions and social rights of landless people in agriculture, be it migrant agricultural workers in Europe or plantation workers in the Global South. The book concludes that despite continuing calls for advancing social justice and decent work with rural economies, landless agricultural workers remain at the bottom of the global value chain.
The futures of Futurism
Authors: Merjian Ara H
Published: February 2025

This chapter considers the future of Futurism. Futurism’s social utopia comprised profoundly dystopian elements from the start, as it preferred violence to the stale certitude of posterity, and its relentless will to progress entailed the movement’s own self-destruction. The chapter explains how Futurism’s founding manifesto fabricated out of sheer will a world unto itself. According to art historian Maurizio Calvesi, Futurism began and ended with an exaltation of machines, which is tantamount to claiming that a Pop sensibility in art exhausted itself with the proliferation of mass media. The chapter also provides an overview of the interplay between Futurism and the internet, as well as the phenomenon of Afrofuturism.
Introduction
Authors: Castater Eric G , Han Kyung Joon
Published: February 2025

This chapter provides an introduction to and an overview of the book. The first section of the chapter reviews major theories on blue-collar worker support for the populist radical right and discusses their shortcomings. The second section outlines the authors’ social identity approach to overcome the pre-existing theories’ shortcomings and account for blue-collar worker support for the populist radical right. The third section introduces empirical strategies to examine how political and economic circumstances of blue-collar workers determine their populist radical right support through their social identity and issue salience. The fourth section discusses implications of the authors’ theory and findings on diverse aspects of politics, such as the crisis of democracy, issues around labour politics, the welfare state, economic inequality, and the politics of the populist radical right. The final section outlines each chapter of the book.
Policy Outputs
Authors: Castater Eric G , Han Kyung Joon
Published: February 2025

This chapter focuses on policy outputs. In particular, it examines employment protection legislation and government spending on labour market policies. It finds that strong employment protection legislation and generous spending on labour market policies decrease blue-collar worker support for populist radical right-wing parties due to a weakened nation-based identity and the decreased salience of cultural issues. Since not all blue-collar workers are in a precarious economic position, the chapter also examines the effect of employment protection legislation and spending on labour market policies on blue-collar workers with and without secure employment, or what it refers to as ‘labour market insiders’ and ‘labour market outsiders’. It finds that employment protection legislation affects the populist radical right support of labour market insiders, but not labour market outsiders; while government spending on labour market policies affects the populist radical right support of labour market outsiders, but not labour market insiders.
Policy Outcomes
Authors: Castater Eric G , Han Kyung Joon
Published: February 2025

This chapter focuses on policy outcomes. In particular, it examines wage inequality between blue-collar and white-collar workers and unemployment inequality between those with and without a college degree. Consistent with theoretical expectations, the chapter finds that high levels of these forms of inequality increase the likelihood that blue-collar workers will support populist radical right-wing parties due to a strengthened nation-based identity and the increased salience of cultural issues. Given that these forms of inequality are particularly harmful for less skilled (and thus less paid) blue-collar workers, the chapter also examines whether their effects differ based on the skill level of blue-collar workers. As anticipated, it finds that higher levels of wage inequality and unemployment inequality increase populist radical right support of less skilled blue-collar workers more than highly skilled blue-collar workers.
Plasma brain-derived neurotrophic factor concentrations are elevated in community-dwelling adults with sarcopenia
Authors: Pratt Jedd , Motanova Evgeniia , Narici Marco V , Boreham Colin , De Vito Giuseppe
Published: February 2025

Background

The scalability of a blood-based sarcopenia assessment has generated interest in circulating markers that may enhance management strategies. Data regarding the relevance of brain derived neurotrophic factor (BDNF), a regulator of neuroplasticity, to sarcopenia in community-dwelling adults are scarce. We examined the association between plasma BDNF concentrations, sarcopenia and individual sarcopenia signatures in a well-characterised adult cohort.

Methods

Participants included 246 men and women aged 50–82 years (mean age = 63.6 years; 52% female). Muscle strength and skeletal muscle index (SMI) were assessed by hand dynamometry and dual-energy X-ray absorptiometry. Plasma BDNF concentrations were determined, in duplicate, with commercially available enzyme-linked immunosorbent assays. Sarcopenia and individual signatures of sarcopenia (i.e. low grip strength or low SMI) were diagnosed according to the EWGSOP2 algorithm.

Results

Plasma BDNF concentrations were 47.6% higher in participants with sarcopenia than controls (P = 0.005), and demonstrated acceptable diagnostic accuracy (areas under the curves = 0.702, 95%CI = 0.597–0.806, P = 0.002, optimal cut-off >1645 pg/ml). Plasma BDNF concentration >1645 pg/ml was associated with 2.83 greater odds for sarcopenia (95%CI = 1.13–7.11, P = 0.027), than ≤1645 pg/ml, whilst a BDNF Z-score ≥2 was associated with 5.14 higher odds for sarcopenia (95%CI = 1.16–22.82, P = 0.031), than a Z-score <1. Covariates included sex, age, body mass index, habitual physical activity, smoking status, alcohol consumption, comorbidity and educational attainment.

Conclusion

Circulating BDNF concentrations are elevated in community-dwelling men and women with sarcopenia, which may reflect increased neuromuscular remodelling in these people. Our findings complement existing data, supporting the presence of an intricate relationship between neural integrity and skeletal muscle health. Future studies are needed to establish the mechanistic pathways that may underpin the associations.
GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions
Authors: Zhang Zhenmiao , Gupta Ishaan , Pevzner Pavel A
Published: February 2025

Motivation

The emergence of the ‘telomere-to-telomere’ genomics brought the challenge of identifying segmental duplications (SDs) in complete genomes. It further opened a possibility for identifying the differences in SDs across individual human genomes and studying the SD evolution. These newly emerged challenges require algorithms for reconstructing SDs in the most complex genomic regions that evaded all previous attempts to analyze their architecture, such as rapidly evolving immunoglobulin loci.

Results

We describe the GenomeDecoder algorithm for inferring SDs and apply it to analyzing genomic architectures of various loci in primate genomes. Our analysis revealed that multiple duplications/deletions led to a rapid birth/death of immunoglobulin genes within the human population and large changes in genomic architecture of immunoglobulin loci across primate genomes. Comparison of immunoglobulin loci across primate genomes suggests that they are subjected to diversifying selection.

Availability and implementation

GenomeDecoder is available at https://github.com/ZhangZhenmiao/GenomeDecoder. The software version and test data used in this paper are uploaded to https://doi.org/10.5281/zenodo.14753844.
An evolutionary tale on clinical trials in hidradenitis suppurativa
Authors: Sayed Christopher J , Shams Rayad B , Midgette Bria , Garg Amit
Published: February 2025

The therapeutic pipeline for moderate-to-severe hidradenitis suppurativa (HS) is robust. Successes and lessons learned have led to improvements in trial designs aimed at avoiding prior pitfalls, as well as high placebo response in HS, which remains a fundamental threat to drug development.

Herein, we review the evolutions in HS trials over the last 20 years with respect to overall design, sample size, diversity in enrolment, inclusion criteria, concomitant medications, rescue therapy, endpoints and statistical design analysis plans. Areas of focus that merit future consideration are also highlighted.
The landscape of autosomal-dominant Alzheimer’s disease: global distribution and age of onset
Authors: Liu Haiyan , Marsh Thomas W , Shi Xinyu , Renton Alan E , Bowling Kevin M , Ziegemeier Ellen , Wang Guoqiao , Cao Yuchen , Aristel Alisha , Li Jessie , Dickson Alexa , Perrin Richard J , Goate Alison M , Fernández Victoria , Day Gregory S , Doering Michelle , Daniels Alisha , Gordon Brian A , Benzinger Tammie L S , Hassenstab Jason , Ibanez Laura , Supnet-Bell Charlene , Xiong Chengjie , Allegri Ricardo , Berman Sarah B , Fox Nick C , Ryan Natalie , Huey Edward D , Vöglein Jonathan , Noble James M , Roh Jee Hoon , Jucker Mathias , Laske Christoph , Ikeuchi Takeshi , Sanchez-Valle Raquel , Schofield Peter R , Chrem Mendez Patricio , Chhatwal Jasmeer P , Farlow Martin , Lee Jae-Hong , Levey Allan I , Levin Johannes , Lopera Francisco , Martins Ralph , Niimi Yoshiki , Rosa-Neto Pedro , Morris John C , Bateman Randall J , Karch Celeste M , Cruchaga Carlos , McDade Eric , Llibre-Guerra Jorge J
Published: February 2025

We present a comprehensive global analysis of genetic variants associated with autosomal-dominant Alzheimer's disease (ADAD). A total of 550 variants in the APP, PSEN1, and PSEN2 genes were identified, of which 279 were classified as pathogenic or likely pathogenic based on ACMG-AMP criteria, utilizing data from the Dominantly Inherited Alzheimer Network (DIAN), literature, and public databases. Symptomatic age at onset (AAO) data was estimated for 227 of these variants, allowing detailed characterization of their frequency, pathogenicity, and AAO. Importantly, 226 variants meet eligibility criteria for inclusion in disease-modifying clinical trials. Furthermore, we demonstrate the predictive value of mean variant AAO and parental AAO in predicting symptomatic AAO, validated against converters who became symptomatic during follow-up in the DIAN Observational Study (DIAN-OBS). This dataset provides critical insights into the global landscape of ADAD and reveals the genetic and AAO heterogeneity of ADAD variants while refining variant trial eligibility criteria.
HTLV Screening of Blood Donations in England Between 2002 and 2021—Comparison of Screening Strategies
Authors: Harvala Heli , Davison Katy , Webster Mhairi , Reynolds Claire , Taylor Graham P
Published: February 2025

Background

Human T-lymphotropic virus (HTLV) is associated with adult T-cell leukemia/lymphoma and myelopathy. Here we present virological and epidemiological data on HTLV screening of blood donations in England between 2002 and 2021, implemented to prevent its transmission via blood transfusion.

Methods

Data on HTLV testing of blood donations was reviewed; it was initially conducted in pools (2002–2012) and subsequently using individual samples (all donors, 2013–2016; first-time donors and non-leucodepleted component donors, 2017–2021). Data included annual number of donations screened, initial and repeat reactives as well as confirmed positives. Further information, such as likely source of infection, was obtained for HTLV-positives.

Results

Over the 20-year study period, a total of 30 679 741 blood donations were screened for HTLV in England. Under pooled screening strategy, the annual rate of repeat reactive donations remained <5:100 000. However, this rate increased to 51:100 000 with individual screening and further to 123:100 000 with selective screening. A total of 5032 samples were repeat reactive, of which 278 were confirmed HTLV-positives. Although the specificity under each scenario exceeded 99.9%, the rate of repeat reactives was around 50-fold higher in individual compared to pooled screening. Most HTLV infected were UK-born, most likely acquired their infection unknowingly through breast feeding or heterosexual intercourse with an individual associated with an HTLV-endemic country.

Conclusions

These data highlight that pooled testing can be advantageous in low-prevalence settings due to its high specificity and reduced non-specific reactivity. Whether pooling is an applicable strategy to tackle the burden of HTLV infection in resource-poor, HTLV-endemic countries requires further investigations.
Single cell RNA sequencing of haematopoietic cells in fresh and frozen human atheroma tissue
Authors: Ahmad Herra , Gopakumar Jayakrishnan , Nachun Daniel C , Ma Lisa , D’Addabbo Jessica , Huang Xianxi , Koyano Tiffany , Boyd Jack , Woo Yi-Ping Joseph , Fong Robyn , Aalami Oliver , Nguyen Patricia K , Jaiswal Siddhartha
Published: February 2025

Aims

Single-cell RNA sequencing (scRNA-seq) is a powerful method for exploring the cellular heterogeneity within human atheroma but typically requires fresh tissue to preserve cell membrane integrity, limiting the feasibility of large-scale biobanking for later analysis. The aim of this study was to determine whether cryopreservation of fragile and necrotic atheroma tissue affects the viability and transcriptomic profiles of haematopoietic cells in subsequent scRNA-seq analysis, enabling the use of cryopreserved atheroma samples for future research.

Methods and results

We performed scRNA-seq on five paired fresh and cryopreserved atheroma samples—three from coronary arteries and two from carotid arteries. Each sample was enzymatically digested, sorted for CD45+ haematopoietic cells, and processed using the 10× Genomics scRNA-seq workflow. Half of each sample was processed immediately, while the other half was cryopreserved in liquid nitrogen for an average of 5 weeks before thawing and processing. In carotid artery samples, we noted the absence of LYVE1+ macrophages, likely due to the loss of the adventitial layer during endarterectomy procedures. Our results indicated that cryopreservation modestly affected cellular integrity, leading to an increase in the relative abundance of mitochondrial RNA in frozen samples. Minimal differences were observed between fresh and cryopreserved samples in uniquely detected transcripts, cell clustering, or transcriptional profiles within haematopoietic populations.

Conclusions

Our study demonstrates that cryopreserved human atheroma samples can be successfully profiled using scRNA-seq, with comparable transcriptomic data to that obtained from fresh samples. These findings suggest that cryopreservation is a viable method for biobanking atheroma tissues, facilitating large-scale studies without the need for immediate sample processing.
MANUDB: database and application to retrieve and visualize mammalian NUMTs
Authors: Biró Bálint , Gál Zoltán , Nagy Zsófia , Garcia Juan Francisco , Batbold Tsend-Ayush , Hoffmann Orsolya Ivett
Published: February 2025

There is an ongoing genetic flow from the mitochondrial genome to the nuclear genome. The mitochondrial sequences that have integrated into the nuclear genome have been shown to be drivers of evolutionary processes and cancerous transformations. In addition to their fundamental biological importance, these sequences have significant consequences for genome assembly and phylogenetic and forensic analyses as well. Previously, our research group developed a computational pipeline that provides a uniform way of identifying these sequences in mammalian genomes. In this paper, we publish MANUDB—the MAmmalian NUclear mitochondrial sequences DataBase, which makes the results of our pipeline publicly accessible. With MANUDB one can retrieve and visualize mitochondrial genome fragments that have been integrated into the nuclear genome of mammalian species.

Database URL: manudb.streamlit.app
Integrated double redo percutaneous valve replacement: simultaneous transcatheter aortic and mitral valve management
Authors: Hinkov Hristian , Lee Chong Bin , Greve Dustin , Klein Christoph , Kukucka Marian , Kempfert Jörg , Jacobs Stephan , Falk Volkmar , Dreger Henryk , Unbehaun Axel
Published: February 2025

OBJECTIVES

The growing elderly population contributes to an increasing prevalence of severe degenerative native aortic valve (AV) or mitral valve (MV) disease in combination with bio-prosthetic valve failure of prior implanted (aortic or mitral) bio-prostheses, as well as concomitant failure of both aortic and mitral bio-prosthetic valves. A combined surgical AV and MV replacement carries a markedly higher risk, especially in the redo setting. Transcatheter double-valve implantation (TDVI) is emerging as a promising alternative that may mitigate the risks of redo surgery. The evidence for TDVI is very limited. This study aims to address the current gap in the literature by analysing a large institutional series of single-stage TDVI.

METHODS

Single-centre retrospective analysis of all patients (n = 13) undergoing simultaneous transcatheter aortic valve implantation (TAVI) and transcatheter mitral valve implantation (TMVI) from October 2018 until April 2024. Primary end-points were Valve Academic Research Consortium-3 (VARC-3) and Mitral Valve Academic Research Consortium (MVARC) technical success, 30-day device success and early safety (MVARC procedural success). Secondary end-points included echocardiographic TDVI performance, adverse events, symptom change and survival.

RESULTS

The median age of patients was 77 years, with 7/13 (53.8%) females. Median EuroSCORE II was 16.9%. All patients presented with structural valve degeneration with severe haemodynamic valve deterioration according to the VARC-3 definition. Procedural outcomes showed 100% technical success. There was absence of 30-day mortality (0%). Thirty-day device success and early safety/MVARC procedural success were 100%. No major adverse events occurred. After TDVI, the median New York Heart Association functional class improved from III to II.

CONCLUSIONS

TDVI appears to be a safe and effective alternative to surgical redo double-valve replacement for selected patients. Our findings support the feasibility of TDVI with excellent early outcomes. Further prospective multicentre studies with larger cohorts are needed to validate the long-term effects and to establish TDVI as a guideline consideration.
Micromix: web infrastructure for visualizing and remixing microbial ‘omics data
Authors: Hayward Regan J , Ebbecke Titus , Fricke Hanna , Nguyen Vo Quang , Barquist Lars
Published: February 2025

Micromix is a flexible web platform for sharing and integrating microbial omics data, including RNA sequencing and transposon-insertion sequencing. Currently, the lack of solutions for making data web-accessible results in omics data being fragmented across supplementary spreadsheets or languishing as raw read data in public repositories. Micromix solves this problem and can be easily deployed on a standard web server or using cloud services. It is organism-agnostic, accommodates data and annotations from various sources, and allows filtering based on KEGG pathways, Gene Ontology terms, and curated gene sets. Visualizations are provided through a plug-in system that integrates existing visualization services and allows rapid development of new services, with available plug-ins currently supporting interactive heatmap and clustering functions. Users can upload their own data in a variety of formats to perform integrative analyses in the context of existing datasets. To support collaborative research, Micromix allows sharing of interactive sessions that maintain defined filtering and/or visualization options. We demonstrate the utility of Micromix with case studies focusing on the SPI-2 pathogenicity island in Salmonella enterica and polysaccharide utilization loci in Bacteroides thetaiotaomicron, showcasing the platform’s capabilities for integrating, filtering, and visualizing diverse functional genomic datasets. Micromix is available at http://micromix.systems.
On the Jurisdictional Situations of Arctic Large Marine Ecosystems
Authors: Soares de Oliveira César , Heinrich Katharina
Published: February 2025

The Arctic Council has identified and delineated 18 large marine ecosystems (LMEs) to provide a basis for the implementation of the ecosystem approach to management (EAM) in the Arctic. However, the ‘natural boundaries’ of these LMEs largely misalign with the ‘artificial boundaries’ established under the United Nations Convention on the Law of the Sea (UNCLOS). This raises the question of how EAM could be effectively implemented across diverse and multiple jurisdictions of the Arctic LMEs. By visualising the so-called jurisdictional situation of all 18 Arctic LMEs, this food-for-thought article highlights the inequitable and delicate position that the zonal approach of UNCLOS creates for the protection of Arctic LMEs.
Metabolite profiles of processed finger millet (Eleusine coracana) and edible crickets (Acheta domesticus) using gas chromatography–mass spectrometry (GC–MS)
Authors: Mahlanza Zamancwane Pretty , Bamidele Oluwaseun Peter , Oyeyinka Samson Adeoye , Sobowale Sunday Samuel , Ledbetter Moira , Wilkin Jon , Adebo Oluwafemi Ayodeji
Published: February 2025

Variations occur in metabolite profiles after food processing, with gas chromatography–mass spectrometry (GC–MS) being one such technique used in profiling metabolites. In this study, finger millet (Eleusine coracana) grains were traditionally (malted and fermented) and also novelly processed (ultra-sonicated), while edible crickets (Acheta domesticus) were fermented and ultra-sonicated. One hundred and nine (109) compounds using gas chromatography–mass spectrometry (GC–MS) in raw and processed finger millet and edible cricket flour were observed and categorized into different metabolite groups: acids, alcohols, amino acids, aromatic compounds, benzene, ethanol, fatty acids, organic acids, and sugars. Significant differences in metabolite profiles, average peak area levels, and the metabolite composition between the finger millet and edible cricket samples before and after traditional and novel processing demonstrate the influence of the processing methods used. Principal component analysis (PCA) observed the relationship among the processing technique’s distribution of metabolite profiles, while OPLS-DA highlighted the significant metabolite profiles observed within the different processing techniques. Differences were observed in the samples as a function of the processing technique used and the modifications, which are attributable to the pre-existing composition of the substrate and the impact of the different techniques, among others. The study’s findings provide a crucial framework for tracking and controlling the metabolite composition of finger millet and edible cricket flours during traditional and novel processing.