julilili42/papers huggingface dataset:
Distributed optical fibre sensing in physical oceanography: Emergence and future prospects
2025-08-08

Abstract. Distributed optical fibre sensing (DOFS) is a technology that enables continuous, real-time measurements of a range of environmental parameters along the length of a fibre optic cable. In this article, we review the recently emerged applications of DOFS techniques in physical oceanography and offer a perspective on the technology’s potential for future growth within the field. The introduction of DOFS to physical oceanography is contextualised with a brief history of the technology, which spun off primarily from the use of seafloor-laid optical fibres for telecommunications purposes. The key components and underpinning physics of a DOFS system are outlined and, on their basis, the suite of variables that are observable with DOFS are discussed. The implementation factors of DOFS, which include trade-offs between measurement accuracy and spatio-temporal resolutions and ranges, are also examined. The physical oceanographic applications of DOFS to date are then illustrated with case examples of three distinct DOFS techniques: distributed temperature sensing (DTS), which can provide ocean temperature observations; distributed acoustic sensing (DAS), which is sensitive to cable strain and associated variables, such as pressure and ocean velocity; and ultra-long-range observations of ocean currents with optical interferometry. The forthcoming prospects of DOFS in physical oceanography are considered, and are proposed to include new fibre optic-based approaches to sense ocean salinity and measure through the water column. We conclude with reflections on the future role of DOFS within the global ocean observing system, and highlight the opportunities provided by the existing world-wide network of seafloor-laid optical fibres.
Associations between epilepsy-related polygenic risk and brain morphology in childhood
2025-08-08

Abstract Extensive neuroimaging research in temporal lobe epilepsy with hippocampal sclerosis (TLE-HS) has identified brain atrophy as a disease phenotype. While it is also related to a complex genetic architecture, the transition from genetic risk factors to brain vulnerabilities remains unclear. Using a population-based approach, we examined the associations between epilepsy-related polygenic risk for HS (PRS-HS) and brain structure in healthy developing children, assessed their relation to brain network architecture, and evaluated its correspondence with case-control findings in TLE-HS diagnosed patients relative to healthy individuals We used genome-wide genotyping and structural T1-weighted magnetic resonance imaging (MRI) of 3,826 neurotypical children from the Adolescent Brain Cognitive Development (ABCD) study. Surface-based linear models related PRS-HS to cortical thickness measures, and subsequently contextualized findings with structural and functional network architecture based on epicentre mapping approaches. Imaging-genetic associations were then correlated to atrophy and disease epicentres in 785 patients with TLE-HS relative to 1,512 healthy controls aggregated across multiple sites. Higher PRS-HS was associated with decreases in cortical thickness across temporo-parietal as well as fronto-central regions of neurotypical children. These imaging-genetic effects were anchored to the connectivity profiles of distinct functional and structural epicentres. Compared with disease-related alterations from a separate epilepsy cohort, regional and network correlates of PRS-HS strongly mirrored cortical atrophy and disease epicentres observed in patients with TLE-HS, and highly replicable across different studies. Findings were consistent when using statistical models controlling for spatial autocorrelations and robust to variations in analytic methods. Capitalizing on recent imaging-genetic initiatives, our study provides novel insights into the genetic underpinnings of structural alterations in TLE-HS, revealing common morphological and network pathways between genetic vulnerability and disease mechanisms. These signatures offer a foundation for early risk stratification and personalized interventions targeting genetic profiles in epilepsy.
In Vitro Modeling of Diurnal Changes in Bone Metabolism
2025-08-08

There is evidence that bone health is closely linked to a functioning circadian rhythm. Most of the evidence comes from mice, which may exhibit some species-specific differences from humans due to their nocturnal lifestyle. To address the current lack of human model systems, the present study aimed to develop an in vitro model system that can represent diurnal changes in bone metabolism. The model is based on co-cultured SCP-1 and THP-1 cells that serve as osteoblast and osteoclast precursors, respectively. Diurnal effects were induced by replacing the FCS in the differentiation medium with human serum pools (HSPs) obtained in the morning, noon, or evening. The model system was tested for cell viability, gene expression, and osteoblast and osteoclast function. The replacement of the FCS with the HSPs increased viability and induced expression changes in circadian clock genes in the model system. Resulting alterations in osteoblast and osteoclast function led to a gradual increase in mineral density and stiffness when 3D co-cultures were differentiated in the presence of the HSPs collected in the morning, noon, or evening, respectively. Here, we present for the first time an in vitro model that can present diurnal changes in bone metabolism in the form of a snapshot. With the simple use of HSPs, this model can be used as a platform technique to investigate bone function in various situations, taking into account the time of day.
Ligatures and their leib-bound and socially mediated leib-bound ties – foundations for an actualization of Ralf Dahrendorf’s concept of life chances with recourse to Karl Popper’s theory of the three worlds and its extension
2025-08-08

This essay deals with the extension of two concepts that have proven themselves in social science research and philosophy, but also have the potential to be applied in other contexts on the one hand, and to enter into a reciprocal connection on the other, namely Ralf Dahrendorf’s life chances approach and Karl Popper’s theory of three worlds. The extension of the Three Worlds Theory concerns the intersubjective, that of the life chances approach the integration of the human leib (as a connection between body and mind) into the concept of ligatures (which, in conjunction with options, form and determine life chances). The leib not only shapes ligatures, but it also mediates social ligatures, so that it has a prominent influence on life chances.
Conserved function, divergent evolution: mitochondrial outer membrane insertases across eukaryotes
2025-08-09

Abstract Mitochondrial function relies heavily on the proper targeting and insertion of nuclear-encoded proteins into the outer mitochondrial membrane (OMM), a process mediated by specialised biogenesis factors known as insertases. These insertases are essential for the membrane integration of α-helical OMM proteins, which contain one or multiple hydrophobic transmembrane segments. While the general mechanisms of mitochondrial protein import are well established, recent research has shed light on the diversity and evolutionary conservation of OMM insertases across eukaryotic lineages. In Saccharomyces cerevisiae , the mitochondrial import (MIM) complex, composed of Mim1 and Mim2, facilitates the integration of various α-helical OMM proteins, often in cooperation with import receptors such as Tom20 and Tom70. In Trypanosoma brucei , the functional MIM counterpart pATOM36 performs a similar role despite lacking sequence and structural homology, reflecting a case of convergent evolution. In mammals, MTCH2 has emerged as the principal OMM insertase, with MTCH1 playing a secondary, partially redundant role. This review provides a comparative analysis of these insertases, emphasising their conserved functionality, species-specific adaptations, and mechanistic nuances.
Measuring Implicit Approach‐Avoidance Tendencies Using Self‐Depicting Body Pictures in Female Adults With Bulimia Nervosa, High Body Dissatisfaction and Healthy Controls
2025-08-09

ABSTRACT Objective Body dissatisfaction is an important factor for the etiology and maintenance of eating disorders such as bulimia nervosa (BN). At the behavioral level, body dissatisfaction often manifests itself in excessive body‐related avoidance, thought to act as a negative reinforcer. The Approach‐Avoidance Task (AAT) is an implicit measure of avoidance behavior, but the literature on body‐related avoidance measured by the AAT is inconclusive. In the present study, we considered self‐reference and cognitive load as important dimensions to better understand AAT‐evoked biases. Method Adult female participants with BN ( n = 21), high body dissatisfaction ( n = 20), and healthy controls ( n = 20) completed a novel, slider‐based AAT with task‐irrelevant self‐depicting body pictures and scrambled versions of these pictures as control stimuli. We further induced cognitive load through a flanker task to assess possible moderating effects. Results There was no significant Group × Picture Type × Motion Direction interaction for either motion onset or motion duration. The results further revealed a standard flanker effect in that participants reacted faster to compatible trials; but this was independent of Group membership, Picture Type, and Motion Direction. Discussion In sum, the AAT did not yield evidence of body‐related avoidance behavior. Future studies should control for the occurrence of body checking (i.e., increased focus on disliked body parts which could activate approach‐biases) during AAT, manipulate the strength of self‐reference, e.g., by presenting/omitting facial cues in self‐depicting body pictures, and consider the task relevance of (and thus overt attention to) the body pictures.
Brain transcriptomics highlight abundant gene expression and splicing alterations in non-neuronal cells in aFTLD-U
2025-08-10

Abstract Atypical frontotemporal lobar degeneration with ubiquitin-positive inclusions (aFTLD-U) is a rare cause of frontotemporal lobar degeneration (FTLD), characterized postmortem by neuronal inclusions of the FET family of proteins (FTLD-FET). The recent discovery of TAF15 amyloid filaments in aFTLD-U brains represents a significant step toward improved diagnostic and therapeutic strategies. However, our understanding of the etiology of this FTLD subtype remains limited, which severely hampers translational research efforts. To explore the transcriptomic changes in aFTLD-U, we performed bulk RNA sequencing on the frontal cortex tissue of 21 aFTLD-U patients and 20 control individuals. Cell-type deconvolution revealed loss of excitatory neurons and a higher proportion of astrocytes in aFTLD-U relative to controls. Differential gene expression and co-expression network analysis, adjusted for the shift in cell-type proportions, showed dysregulation of mitochondrial pathways, transcriptional regulators, and upregulation of the Sonic hedgehog (Shh) pathway, including the GLI1 transcription factor, in aFTLD-U. Overall, oligodendrocyte and astrocyte-enriched genes were significantly over-represented among the differentially expressed genes. Differential splicing analysis confirmed the dysregulation of non-neuronal cell types with significant splicing alterations, particularly in oligodendrocyte-enriched genes, including myelin basic protein ( MBP ), a crucial component of myelin. Immunohistochemistry in frontal cortex brain tissue also showed reduced myelin levels in aFTLD-U patients compared to controls. Together, these findings highlight a central role for glial cells, particularly astrocytes and oligodendrocytes, in the pathogenesis of aFTLD-U, with disruptions in mitochondrial activity, RNA metabolism, Shh signaling, and myelination as possible disease mechanisms. This study offers the first transcriptomic insight into aFTLD-U and presents new avenues for research into FTLD-FET.
PanBGC: A Pangenome-inspired framework for comparative analysis of biosynthetic gene clusters
2025-08-11

A bstract Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce PanBGC , a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. To facilitate exploration, we present PanBGC-DB ( https://panbgc-db.cs.uni-tuebingen.de ), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring biosynthetic gene clusters at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.
Rationale and design of the TRIC ‐I‐ HF ‐ DZHK24 ( TRICuspid Intervention in Heart Failure) trial
2025-08-11

Abstract Aims Tricuspid regurgitation ( TR ) is a detrimental disease frequently diagnosed in patients with right‐sided heart failure ( HF ). While transcatheter tricuspid valve interventions ( TTVI ) effectively reduce TR and improve quality of life ( QoL ) in earlier stages of the disease, their effect on reducing HF hospitalizations ( HFH ) and improving survival remains unclear. Methods TRIC‐I‐HF‐DZHK24 (NCT04634266) is an investigator‐initiated, prospective, randomized, open‐label, multicentre strategy trial. Approximately 360 patients with severe TR and manifest right‐sided HF will be enrolled. In contrast to previous trials, subjects with increased risk for HFH will be selected as facilitated by specific inclusion criteria: HFH in the previous year, or presence of cardio‐renal syndrome, or evidence for cardio‐hepatic syndrome. Subjects will be randomized 2:1 to TTVI and optimal medical therapy (OMT) or continuation of OMT alone. All CE‐marked transcatheter repair devices including tricuspid transcatheter edge‐to‐edge repair (T‐TEER) or transcatheter tricuspid annuloplasty can be used for TTVI. The participating 29 study sites are highly experienced and treated a mean of 176 patients in 4.5 years with T‐TEER before study activation. The primary outcome will be assessed at 1 year. First, a composite of all‐cause mortality, HFH, and QoL improvement will be tested hierarchically. If positive, the combination of hard clinical endpoints including all‐cause mortality and HFH will be tested. Patients will be followed for a total of 3 years. The safety outcome comprises complications of TTVI, life‐threatening bleeding and death. Conclusions The TRIC‐I‐HF‐DZHK24 trial will define the role of TTVI in patients with severe TR and right‐sided HF.
Reduced Amino Acid Substitution Matrices Find Traces of Ancient Coding Alphabets in Modern Day Proteins
2025-08-11

Abstract All known living systems make proteins from the same 20 canonically coded amino acids, but this was not always the case. Early genetic coding systems likely operated with a restricted pool of amino acid types and limited means to distinguish between them. Despite this, amino acid substitution models like LG and WAG all assume a constant coding alphabet over time. That makes them especially inappropriate for the aminoacyl-tRNA synthetases (aaRS)—the enzymes that govern translation. To address this limitation, we created a class of substitution models that account for evolutionary changes in the coding alphabet size by defining the transition from 19 states in a past epoch to 20 now. We use a Bayesian phylogenetic framework to improve phylogeny estimation and testing of this two-alphabet hypothesis. The hypothesis was strongly rejected by datasets composed exclusively of “young” eukaryotic proteins. It was generally supported by “old” (aaRS and non-aaRS) proteins whose origins date from before the last universal common ancestor. Standard methods overestimate the divergence ages of proteins that originated under reduced coding alphabets in both simulated and aaRS alignments. The new model provides a timeline slightly more consistent with the Earth’s history. Our findings suggest that aaRS functional bifurcation events can explain much of the genetic code’s evolution, but there remain other unknown forces at play too. This work provides a robust, seamless framework for reconstructing phylogenies from ancient protein datasets and offers further insights into the dawn of molecular biology.
Environment-mediated interactions cause an externalized and collective memory in bacteria
2025-08-11

Abstract Bacteria usually live in complex communities interacting with many other microbial species. These interactions determine who can persist in a community and how the overall community forms and functions. Bacteria often exert interactions by chemically changing the environment, like taking up nutrients or producing toxins. These environmental changes can persist over time. We show here that such lasting environmental changes can cause a “memory effect” where current growth conditions alter interaction outcomes in the future. This memory is only stored in the environment and not inside bacterial cells. Only the collective effort of many bacteria can build up this memory, making it an emergent property of bacterial populations. This externalized and collective memory can also impact the assembly of more complex communities and lead to different final compositions depending on the system's past. Overall, we show that to understand interaction outcomes fully, we not only have to consider the interacting species and abiotic conditions but also the system's history.
Ultra-luminous X-ray pulsars as sources of TeV neutrinos
2025-08-11

We explored the expected properties of the neutrino emission from accreting neutron stars in X-ray binaries using numerical simulations. The simulations are based on a model in which neutrinos are produced by the decay of charged pions and kaons, generated in inelastic collisions between protons accelerated up to TeV energies in the magnetosphere of a magnetized ( B ∼ 10 12 G) neutron star and protons of the accretion disc. Our results show that this process can produce strong neutrino emission up to a few tens of TeV when the X-ray luminosity is above ∼10 39 erg s −1 , as in ultra-luminous X-ray (ULX) pulsars. We show that neutrinos from a transient Galactic ULX pulsar with L x ≈ 5 × 10 39 erg s −1 can be detected with kilometre-scale detectors such as IceCube if the source is within about 3–4 kpc. We also derived an upper limit on the neutrino flux from the Galactic ULX pulsar Swift J0243.6+6124 using IceCube data, a result that has not been previously reported. Our findings establish a new benchmark for future astrophysical neutrino observations, critical for interpreting data from current and upcoming instruments with significantly improved sensitivity.
Between Bible and Byzantium: “Corruption on Earth” (fasād fī l-arḍ) and the Qur’an’s Penal Code (Q 5:33-34.38-39)
2025-08-11

Abstract This two-partite article begins with a summary account of the Qur’an’s legal culture, and then examines the qur’anic concept of “causing corruption,” afsada , particularly “causing corruption on earth” ( fasād fī l-arḍ ). First, it situates this concept within the Qur’an’s semantic and linguistic framework, and second, it analyzes the related qur’anic penal legislation for “causing corruption” (Q 5:33–34) in its biblical, rabbinic, and Byzantine contexts. The article posits that the Qur’an’s penal code is intrinsically linked to its creation theory, which designates the entire earth a Holy Land in which no crime is permissible. The Qur’an’s categorization of actions that cause corruption, moreover, both resonate with and further develop Genesis 6, which warns against the “corruption of earth,” i. e. of God’s creation, and, more concretely, Leviticus 19–26, which more narrowly focuses on the Land of Israel as God’s Holy Land. In accordance with its biblical precedent, the Qur’an also draws upon biblical, Jewish, and notably Christian paradigms when articulating punishments for those who “wage war against God and his messengers” in Q 5:33–34. It equates such an attack – likely alluding to a recent raid on the qur’anic community in Medina – with “trying to cause corruption on earth” thereby posing a threat to God’s order of creation. When stipulating the appropriate penalty for such corruption, the Qur’an’s phrasing closely mirrors the Aramaic rendition of punishments detailed in 2 Samuel 4:12, where David executes two of his officers for slaying a disabled enemy in his sleep: either exile, crucifixion, or the amputation of hands and feet. A similar list of punishments in Justinian’s criminal law, Novel 134 (promulgated in 556 CE), omits crucifixion but offers an extended parallel to the Qur’an by limiting hand amputation for thieves, contrasting with the sequel of the Qur’an’s penal code in Q 5:38–39. In both cases – the concept of “corruption on earth” and the corresponding punishments – it is challenging to ascertain the extent to which the Quran directly engages with the Hebrew Bible versus its interpretation through Jewish and Christian lenses. Nevertheless, the broad parallels amidst nuanced differences underscore that the prophet’s Hejazi community actively engaged with prevailing legal practices and discourses among Jews and Christians in the Byzantine Empire’s eastern provinces.
The VHB-Rating 2024—more than Just Another Rating
2025-08-11

Abstract The VHB (German Academic Association for Business Research) has released a new rating for publication media, known as VHB-Rating 2024. Even though there was agreement that the previous rating required renewal, specifying the rating terms with regard to the needs of all scientific commissions of the VHB was a challenging process. The aim of this paper is to review the fundamental discussion on journal ratings, outline the VHB’s objectives for the new VHB-Rating 2024, describe the negotiation process leading up to finding a solution, explain the solution found and its implementation and critically discuss the rating results.