bluuebunny/crossref_metadata_2025 huggingface dataset:
The KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells
Authors: Cribbs Adam P , Hookway Edward S , Yapp Clarence , Che Ka-Hing , Dunford James E , Gutheridge Karina , Lari Federica , Wells Graham , Philpott Martin , Cain Peter , Brotherton Deborah , Palmer Charlotte , Maret Wolfgang , Fitzgibbons Jude , Christianson John C. , Oppermann Udo
Published: December 2024

Thioneins are cysteine-rich apoproteins that regulate divalent metal homeostasis by virtue of their metal-chelation properties resulting in the ligand-bound metallothionein state. Previous studies show transient upregulation of the metallothionein (MT) gene cluster as part of a complex transcriptional response to a class of histone demethylase tool compounds targeting human Fe2+dependent ketoglutarate oxygenases KDM6A (UTX) and KDM6B (JmjD3). The prototypic bioactive KDM6 inhibitor GSK-J4 induces apoptotic cell death in multiple myeloma cells and corresponding transcriptomic profiles are dominated by metal and metabolic stress response signatures, also observed in primary human myeloma cells. Here we investigate the hypothesis that metal-chelation by GSK-J4 provides the means for transport and intracellular release of Zn2+leading to a metallothionein transcriptomic response signature. Live cell imaging of myeloma cells shows transient increases in intracellular free Zn2+concentrations when exposed to GSK-J4, consistent with a model of inhibitor-mediated metal transport. Comparisons of GSK-J4 and ZnSO4treatments in the presence or absence of metal chelators show that both treatment conditions induce different transcription factor repertoires with an overlapping MTF1 transcriptional regulation responsible for metallothionein and metal ion transport regulation. The data provide a possible explanation for the observed metal response upon GSK-J4 inhibition however the relationship with the pro-apoptotic mechanism in myeloma cells requires further investigation.
Eliminating Aggressive Cancers via PROTAC-like Inducers of Ferroptosis
Authors: Oknin-Vaisman Avital , Panda Deepanjan , Novak Rostislav , Bitman-Lotan Eliya , Pahor Nikolett , Ahmed Yamen Abu , Kamnesky Guy , Diefenbacher Markus E. , Brik Ashraf , Orian Amir
Published: December 2024

Aggressive and therapy-resistant cancers present a significant challenge to treatment and are associated with poor patients’ survival. Identifying molecular pathways and compounds that target these pathways is critical for improving patient outcomes. RNF4, an E3-ubiquitin ligase, is pivotal in oncoprotein stabilization and DNA repair, enhancing cancer cell survival driving tumorigenesis. Elevated RNF4 levels are associated with poor prognosis in cancer patients. Here, we describe the development of R4VPs, proteolysis-targeted chimeras-like (PROTACs-like). R4VPs promote RNF4 degradation and reduce the levels of its stabilized oncoproteins. Notably, R4VPs induce ferroptotic cell death selectively in cancer cells, sparing non-tumorigenic and primary cells. Surprisingly, R4VPs-induced ferroptosis is independent of RNF4 but preferentially targets tumor-driving mutations, particularly those in the EGFR pathway, while not affecting PI3K-transformed cells. R4VPs effectively induce cell death in therapy-resistant melanoma and sarcomas including patient-derived sarcoma tumor cells. Our findings highlight the potential of ferroptosis inducers such as R4VPs as a therapeutic strategy for therapy resistance, aggressive, and hard-to-treat cancers.

Teaser

R4VPs induce ferroptotic death of melanoma and sarcoma cells including patient-derived tumor cells sparing non-transomed cells.
Base edited “universal” donor CAR T cell strategies for acute myeloid leukaemia
Authors: Kadirkamanathan Renuka , Georgiadis Christos , Kloos Arnold , Etuk Annie , Preece Roland , Gough Oliver , Schambach Axel , Sauer Martin , Heuser Michael , Qasim Waseem
Published: December 2024

Acute myeloid leukaemia (AML) is often aggressive and life-threatening with limited curative options. Immunotherapies including chimeric antigen receptor (CAR) T cell approaches are under investigation, but high levels of disease heterogeneity remain a major hurdle to achieving durable responses. Targeting of multiple surface antigens may ensure complete immunological coverage of leukemic blast populations, but such antigens are often also present on healthy haematopoietic populations. To address likely aplasia, strategies can be designed to bridge CAR T cell therapies to allogeneic stem cell transplantation (allo-SCT), as demonstrated in recent anti-CD7 CAR T cell studies. Here we report that monotherapy using base edited (BE) ‘universal’ donor CAR T cells against CD33, CLL-1, or CD7 delivered inhibition of AML in immunodeficient mice when antigen expression was homogenous, but combined use of BE-CAR33 and BE-CARCLL-1 T cells was required to address heterogenous CLL-1-/+CD33-/+disease. We also demonstrate that removal of shared CD7 antigens enabled compatibility of BE-CAR33 with BE-CAR7 T cells, including in a patient-derived xenograft (PDX) model of AML. Therapeutic strategies envisage ‘pick and mix’ applications of base edited universal CAR T cells in combinations determined by patient-specific antigen profiles. Such approaches also offer the possibility of deep, cell-based, de-bulking and preparative conditioning ahead of allo-SCT followed by donor-derived reconstitution.
Dynamic Coupling and Entropy Changes in KRAS G12D Mutation: Insights into Molecular Flexibility, Allostery and Function
Authors: Hacisuleyman Aysima , Yuret Deniz , Erman Burak
Published: December 2024

The oncogenic G12D mutation in KRAS is a major driver of cancer progression, yet the complete mechanism by which this mutation alters protein dynamics and function remains incompletely understood. Here, we investigate how the G12D mutation alters KRAS’s conformational landscape and residue-residue interactions using molecular dynamics simulations coupled with entropy calculations and mutual information (MI) analysis. We demonstrate that the mutation increases local entropy at key functional residues (D12, Y32, G60, and Q61), and introduces new peaks to the Ramachandran angles, disrupting the precise structural alignment necessary for GTP hydrolysis. Notably, while individual residue entropy increases, joint entropy analysis shows a complex reorganization pattern. MI analysis identifies enhanced dynamic coupling between distant residues, suggesting that the mutation establishes new long-range interactions that stabilize the active state. These findings show how G12D mutation redefines KRAS’s dynamic network, leading to persistent activation through enhanced residue coupling rather than mere local disruption. Our results suggest novel therapeutic strategies focused on modulating protein dynamics rather than targeting specific binding sites, potentially offering new approaches to combat KRAS-driven cancers.

Highlights

The G12D mutation increases entropy and mutual information between residue pairs, resulting in more correlated motions due to enhanced flexibility.

Characteristic features of local and long-range allostery in wild-type (WT) and G12D KRAS are determined using structural proximity and mutual information analysis.

The dynamics of KRAS interactions with its natural ligand atoms and the coordination of bridging water molecules provide insights into the changes induced by the G12D mutation.
Molecular determinants underlying differential recruitment of p115RhoGEF and PDZRhoGEF to activated Gα13
Authors: Fassler Bakhman Anna , Lukasheva Viktoriya , Le Gouill Christian , Kosloff Mickey , Bouvier Michel
Published: December 2024

Heterotrimeric G proteins, particularly Gα12and Gα13, are pivotal regulators of cellular signaling pathways. Their direct downstream effectors, which include p115RhoGEF and PDZRhoGEF, engage downstream signaling via Rho activation. Yet the molecular determinants that dictate their differential recruitment by Gα12/13are not fully understood. Here, we combined quantitative computational residue-level analysis with site-directed mutagenesis and bioluminescence resonance energy transfer (BRET)-based assays to dissect Gα13interactions with these RhoGEFs. We mapped the contributions of individual residues to binding and identified specific Gα13residues in its helical domain, switch regions, and effector-binding site as key yet differential contributors to p115RhoGEF and PDZRhoGEF recruitment. Experimental validation with BRET confirmed that changes in many Gα13residues impact p115RhoGEF more substantially than PDZRhoGEF, underscoring the specificity of Gα13interactions with p115RhoGEF. Investigation of the p115RhoGEFs identified critical residues that contribute to interactions with Gα13and Gα12. Our findings highlight residue-level differences in the molecular interactions of Gα13with p115RhoGEF and PDZRhoGEF, providing insights into the specificity and regulation of Gα13-mediated signaling pathways. The resulting residue-level maps lay the groundwork for development of selective therapeutic strategies targeting Gα13-RhoGEF interactions.
Multifaceted B-cell response to transient HIV viraemia in elite controllers
Authors: Muir Luke , Suchanek Ondrej , Thomas Peter , Griffith Sarah A. , Touizer Emma , Rees-Spear Chloe , Yoshida Masahiro , Pinder Christopher L. , Nikolic Marko Z. , Doores Katie J. , Van Gils Marit J. , Gupta Ravindra K. , Clatworthy Menna R. , McCoy Laura E.
Published: December 2024

Chronic HIV infection drives B-cell dysfunction associated with the accumulation of tissue-like memory (TLMs) and activated memory B cells (MBCs) but decline in resting memory B cells. TLMs express multiple inhibitory receptors and lack response to soluble antigens. However, their origin and the mechanisms driving their expansion in HIV infection remain unclear. By using bulk BCR sequencing of memory B cell subsets from elite HIV controllers and an ART-controlled cohort, we revealed that TLMs (CD21-CD27-B cells) were significantly less mutated but also less diverse than other MBCs, suggesting an enrichment for innate-like B cells or that they belong to a less mature subset. Subsequent detailed multi-omics study of an immune response in an elite controller to a transient HIV viraemia demonstrated a functional increase in Env-reactive IgG and MBCs with non-TLM phenotype. Single-cell RNA/BCR sequencing of PMBCs enriched for B cells revealed an orchestrated TNF-alpha response followed by interferon alpha and gamma response across all B cells subsets. We noted an emergence of innate-like extrafollicular PLD4+ plasmablasts and previously undepreciated heterogeneity of a stable TLM population. We identified two distinct TLM subsets: TLM1 (T-betlow) and TLM2 (T-bethi) that differed in their differentiation stage, isotype use and mutational burden. Surprisingly, both subsets (TLM1 more than TLM2) were enriched for IGHV4-34 segment use (associated with self-reactivity) and displayed a persistent activation and BCR signalling signature, indicating (with other BCR indices) a strong presence of innate-like B cells. However, pseudotime analyses revealed that TLMs contained not only innate-like B cells but also cells from the conventional memory B cell lineages, further highlighting the complexity of the whole TLM compartment. This study provides a new insight into multifaceted functional B-cell response to transient HIV viraemia as likely happens during the early phase of anti-retroviral therapy cessation, highlighting the TLM heterogeneity and the contribution of innate-like B cells which might have important clinical implications for anti-HIV vaccine and therapy design.
Volitional stopping is preceded by a transient beta oscillation
Authors: Doutel Figueira Joana F. , Ojala Reetta A. , Vasilev Dmitrii , De Miguel Alejandro , Jeay-Bizot Lucas , Iwai Ryo , Raposo Isabel , Safaei Negar , de Sardenberg Schmid Lilian , Maoz Uri , Watanabe Masataka , Totah Nelson K.
Published: December 2024

Human motor cortex EEG beta (15-30 Hz) oscillations undergo transient power modulations (bursts) during volitional control of movements. They are a potential control signal for brain-machine interfaces and are a therapeutic target in Parkinson’s disease. The prevailing view is that EEG beta bursts increase during stopping and immobility, but do not precede stopping. In contrast to prior work in humans and animals that used a latent and unobservable stopping time in the stop-signal task, we developed a translational animal model to align EEG with overt action stopping. We recorded 32-electrode EEG along with the angular velocity of a treadmill while head-fixed rats stopped in-progress running on a freely-rotating, non-motorized treadmill. Contrasting prior work, motor cortex beta bursts increased before stopping and not during stopping or immobility. Using information theoretic measures, we show that beta power was informative about treadmill velocity 200 msec in the future, but only during planning to stop. By introducing artificial temporal jitter to mimic the estimation of stopping time used in prior work, we show that this predictive brain-action relationship fails with even small jitter. Finally, we use a variety of machine learning methods to show that, despite EEG beta oscillations being a clear neural correlate preceding stopping, it has limited utility for real-time action decoding. Our work suggests a new conceptual model for neural control of action stopping.
Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development inVibrio anguillarum
Authors: Chen Ling , Middelboe Mathias , Svenningsen Sine Lo
Published: December 2024

Exposure of bacterial populations to phage infection pressure is a significant driver of phage-host co-evolution and diversification. However, the impact of the spatial organization of bacterial population ‘co-existence and co-evolution dynamics remains poorly understood. Here, we investigated how the spatial structure of the host population affects phage-host interactions by co-cultivating aVibrio anguillarumstrain with the lytic T4-like vibriophage KVP40 under conditions that resulted in either a homogenous, well-mixed population or a heterogeneous population with bacterial aggregates. We observed markedly different temporal dynamics associated with the two population structures over a 30-day adaptive laboratory evolution experiment. Phage and host dynamics suggested that phage-sensitive subpopulations retained in the aggregates substantially prolonged the coexistence of phages and bacteria, relative to the homogenous environment. However, the limited phage propagation on the sensitive subpopulations was insufficient for host range expansion to occur. In contrast, daily supplementation of sensitive host bacteria in parallel experiments readily led to the emergence of phage mutants with enhanced infective capability and an expanded host range. These results underscore the importance of bacterial spatial organization in determining the outcome of phage attacks and highlight the complex interplay between genomic processes and ecological conditions in driving evolutionary innovations.
Interaction between native and prosthetic visual responses in optogenetic visual restoration
Authors: Carpentiero Eleonora , Hughes Steven , Rodgers Jessica , Xhaferri Nermina , Biswas Sumit , Gilhooley Michael J , Hankins Mark W , Lindner Moritz
Published: December 2024

Degenerative retinal disorders leading to irreversible photoreceptor death are a common cause of blindness. Optogenetic gene therapy aims to restore vision in affected individuals by introducing light sensitive opsins into the surviving neurons of inner retina. While up until now the main focus of optogenetic therapy has been on terminally blind individuals, treating at stages where residual native vision is present could have several advantages. Yet, it is still unknown how residual native and optogenetic vision would interact if present at the same time.

Using transgenic mice expressing the optogenetic tool ReaChR in ON-bipolar cells, we herein examine this interaction through electroretinography (ERG) and visually evoked potentials (VEP). We find that optogenetic responses show a peculiar ERG signature and are enhanced in retinas without photoreceptor loss. Conversely, native responses are dampened in the presence of ReaChR. Moreover, in VEP recordings we find that optogenetic responses reach the cortex asynchronous to the native response.

These findings should be taken into consideration when planning future clinical trials and may direct future preclinical research to optimize optogenetic approaches for visual restoration. The identified ERG signatures moreover may serve to track treatment efficiency in clinical trials.
Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis)
Authors: Soni Vivak , Versoza Cyril J. , Terbot John W. , Jensen Jeffrey D. , Pfeifer Susanne P.
Published: December 2024

The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species, but also across individual genomes. Despite previous studies having demonstrated that failing to account for rate heterogeneity across the genome can bias the inference of both selective and neutral population genetic processes, mutation and recombination rate maps have to date only been generated for a relatively small number of organisms. Here, we infer such fine-scale maps for the aye-aye (Daubentonia madagascariensis) – a highly endangered strepsirrhine that represents one of the earliest splits in the primate clade, and thus stands as an important outgroup to the more commonly-studied haplorrhines – utilizing a recently released fully-annotated genome combined with high-quality population sequencing data. We compare our indirectly inferred rates to previous pedigree-based estimates, finding further evidence of relatively low mutation and recombination rates in aye-ayes compared to other primates.
A new metoposaurid (Temnospondyli) bonebed from the lower Popo Agie Formation (Carnian, Triassic) and an assessment of skeletal sorting in temnospondyls
Authors: Kufner Aaron M. , Deckman Max E. , Miller Hannah R. , So Calvin , Price Brandon R. , Lovelace David M.
Published: December 2024

Metoposaurid-dominated bonebeds are relatively commonplace in Upper Triassic continental deposits with at least ten monodominant, densely populated bonebeds globally. The biostratinomy of several classic localities in India, North America, and Poland have been explored in detail, however, variability in methods and resultant conclusions point to the need for a more nuanced approach to understanding both the taphonomic and the ecological origins of metoposaurid-dominated bonebeds. Here we present the first monodominant metoposaurid mass mortality assemblage from the Late Triassic Popo Agie Formation and the stratigraphically lowest known record of several fauna from the Popo Agie Fm including the first occurrence of theBuettnererpeton bakeriin Wyoming. We employ previously used binning methods based on perceived hydrodynamic equivalence (“Voorhies groups”) to assess pre-burial skeletal sorting. We suggest a simple counting and normalization method that avoids the inherent bias introduced by the interpretation of hydrodynamic equivalence of skeletal elements in taxa that lack actualistic experimental data. In contrast to other North American metoposaurid bonebeds, the sedimentology and skeletal sorting analyses of the Nobby Knob quarry support an autochthonous origin of this assemblage in a fluvio-lacustrine system with relatively little pre-burial sorting. Despite differences in underlying assumptions regarding the dispersal potential of specific skeletal elements, binning methods tend to follow similar trends regardless of framework used to assess different assemblages.
Apolipoprotein-L1 G1 variant contributes to hydrocephalus but not to atherosclerosis in apolipoprotein-E knock-out mice
Authors: Yoshida Teruhiko , Yang Zhi-Hong , Ashida Shinji , Xi Yu Zu , Shrivastav Shashi , Rojulpote Krishna Vamsi , Bahar Piroz , Nguyen David , Springer Danielle A. , Munasinghe Jeeva , Starost Matthew F. , Hoffmann Victoria J. , Rosenberg Avi Z. , Bielekova Bibi , Wen Han , Remaley Alan T. , Kopp Jeffrey B.
Published: December 2024

Introduction

In USA, six million individuals with Sub-Saharan ancestry carry twoAPOL1high-risk variants, which increase the risk for kidney diseases. Whether APOL1 high-risk variants are independent risk factors for cardiovascular diseases is unclear and requires further investigation.

Methods

We characterized a mouse model to investigate the role of APOL1 in dyslipidemia and cardiovascular diseases. Transgenic mice carrying APOL1 (G0 and G1 variants) on bacterial artificial chromosomes (BAC/APOL1 mice) were crossed with the ApoE knock-out (ApoE-KO) atherosclerosis mouse model. The compound transgenic mice were evaluated for the impact of APOL1 on systemic phenotypes.

Results

ApoE-KO mice carrying APOL1-G0 and APOL1-G1 did not show differences in the extent of atherosclerotic lesions or aortic calcification, as evaluated by Sudan IV staining and radiographic examination, respectively. However, ∼20% of ApoE-KO; BAC/APOL1-G1 mice developed hydrocephalus and required euthanasia. The hydrocephalus was communicating and likely was due to excess cerebrospinal fluid produced by the choroid plexus, where epithelial cells expressed APOL1. Single-nuclear RNA-seq of choroid plexus identified solute transporter upregulation and mTORC2 pathway activation in APOL1-G1-expressing epithelial cells. Further, in the All of Us cohort, we found higher hydrocephalus prevalence among individuals with theAPOL1-G1variant in both recessive and dominant models, supporting the mouse findings.

Conclusion

While APOL1-G1 expression in ApoE-KO mice did not worsen cardiovascular disease phenotypes, we uncovered hydrocephalus as a novel APOL1 risk allele-mediated phenotype. These findings extend the spectrum of APOL1-associated pathologies.
Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation
Authors: Su Yue , Zhao Ruifeng , Fang Yifei , Li Guangsheng , Jin Liangliang , Liu Jiaxi , Yang Zhen , Li Ningxiao , Zhu Jiaqi , Mishra Neha , Kaback Deborah , Yee Siu Pok , Lei Chuzhao , Duan Jingyue (Ellie) , Tian Xiuchun (Cindy) , Tang Young
Published: December 2024

Bovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent bothin vitroandin vivo,and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types in both embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism ofbona fidebovine pluripotency.
Leveraging machine learning and accelerometry to classify animal behaviours with uncertainty
Authors: Agarwal Medha , Rafiq Kasim , Mehta Ronak , Abrahms Briana , Harchaoui Zaid
Published: December 2024

Animal-worn sensors have revolutionised the study of animal behaviour and ecology. Accelerometers, which measure changes in acceleration across planes of movement, are increasingly being used in conjunction with machine learning models to classify animal behaviours across taxa and research questions. However, the widespread adoption of these methods faces challenges from imbalanced training data, unquantified uncertainties in model outputs, shifts in model performance across contexts, and noisy classifications.

To address these challenges, we introduce an open-source approach for classifying animal behaviour from raw acceleration data. Our approach integrates machine learning and statistical inference techniques to evaluate and mitigate class imbalances, changes in model performance across ecological settings, and noisy classifications. Importantly, we extend predictions from single behaviour classifications to prediction sets –collections of probable behaviours with a user-specified likelihood of containing the true behaviour – in a framework analogous to the use of confidence intervals in statistical analyses.

We highlight the utility of our approach using data collected from a free-ranging large carnivore, African wild dogs (Lycaon pictus),in the Okavango Delta, Botswana. We demonstrate significantly improved predictions along with associated uncertainty metrics in African wild dog behaviour classification, particularly for rare and ecologically important behaviours such as feeding, where correct classifications more than doubled following quality checks and data rebalancing introduced in our pipeline.

Our approach is applicable across taxa and represents a key step towards advancing the burgeoning use of machine learning to remotely observe around-the-clock behaviours of free-ranging animals. Future work could include the integration of multiple data streams, such as accelerometer, audio, and GPS data, for model training and could be incorporated directly into our pipeline.
Aniline Dioxygenase inRhodococcus ruberR1: Insights into Skatole Degradation
Authors: Galaz S.J. , Saavedra B. , Zúñiga A. , González-Toro F. , Donoso R.
Published: December 2024

Skatole is an aromatic heterocyclic compound with a strong offensive odor, produced by microorganisms during the anaerobic breakdown of tryptophan. Skatole accumulation is linked to environmental and health issues. Despite its persistence and harmful effects, skatole’s biodegradation by microorganisms is poorly understood. We have recently isolated a gram-positive bacterium,Rhodococcus ruberR1, which uses skatole as its sole carbon and energy source. Here we report an operon consisting of 14 genes encoding aromatic oxygenase systems involved in skatole degradation inRhodococcus ruberR1. Cells growing on skatole accumulate aniline transiently, indicating its role as an intermediate in the degradation pathway. We characterize six genes in this cluster that encode for an aniline dioxygenase, which converts aniline to catechol and is only activated in the presence of skatole. This gene cluster was successfully introduced into a heterologous strain enabling the full degradation of aniline and its derivatives. Phylogenetic analysis of aniline dioxygenase present in R1 strain reveals a widespread distribution of this system among bacteria, in contrast to the full skatole cluster, which is restricted to a few genera. These findings advance our understanding of the skatole degradation pathway and highlight R1’s potential for bioremediation of skatole, aniline, and related contaminants.
QC4Metabolomics: Real-time and Retrospective Quality Control of Metabolomics Data
Authors: Stanstrup Jan , Dragsted Lars Ove
Published: December 2024

Motivation

The ability to answer complex biological questions in metabolomics relies on the acquisition of high-quality data. However, due to the complex nature of liquid chromatography–mass spectrometry acquisition, data quality checks are often not done comprehensively and only at the post-processing step. This can be too late to mitigate analytical problems such as loss ofm/zcalibration, retention time drift and severe ion suppression. It is often not practically or economically feasible to reanalyze samples, and interpretation of the acquired compromised data, if at all possible, is limited, despite the considerable expenses incurred to obtain them.

Results

We therefore introduceQC4Metabolomics, a real-time quality control monitoring software for untargeted metabolomics data.QC4Metabolomicsmonitors files as they are acquired or retrospectively by tracking any user-defined compound(s) and extracting diagnostic information such as observedm/z, retention time, intensity and peak shape, and presents the results on a web dashboard.QC4Metabolomicsalso monitors the levels of common or user-defined contaminants. We report herein real-world examples whereQC4Metabolomicseasily reveals analytical problems retrospectively that could have been immediately addressed with real-time monitoring, so that the samples would have been analyzed without any quality control issues.

Availability and Implementation

QC4Metabolomicsis available as code athttps://github.com/stanstrup/QC4Metabolomics. ADockerimage, adocker-composesetup file and demo data are also provided for easy deployment.
Barcoding-inferred biodiversity of shallow-water Indo-Pacific demosponges
Authors: Erpenbeck Dirk , Galitz Adrian , Berumen Michael L. , Büttner Gabriele , Debitus Cécile , Dirnberger Moritz , Ekins Merrick , Hall Kathryn , Namuth Leonard , Petek Sylvain , Rahnamae Neda , Reddy Maggie M. , Rettenberger Daniela , Ries Stefanie R. , Schätzle Simone , Schönberg Christine H.L. , Setiawan Edwin , van der Sprong Joëlle , Thomas Olivier P. , Tirumalasetty Vani , de Voogd Nicole J. , Voigt Oliver , Hooper John N.A. , Wörheide Gert
Published: December 2024

Aim

The Indo-Pacific is the world’s largest marine biogeographic region. It is characterised by different degrees of connectivity among its subregions, and harbours the majority of demosponge species currently known to science. Comparisons between several regional sponge faunas have been undertaken in the past, mostly based on identifying the sponge species morphologically. The Sponge Barcoding Project, in tandem with other regional DNA taxonomy campaigns, provides one of the largest DNA-based taxonomic data collections from sponges of the Indo-Pacific. Here, we utilise the sponge barcoding data in the largest molecular biodiversity study of sponges to date, which reveals patterns of shallow-water demosponge faunal connectivity, endemism, and distribution in the Indo-Pacific with a level of resolution unavailable in prior morphology-based studies.

Location

Demosponge specimens in this study cover 13 marine provinces of the Indo-Pacific, from the Red Sea to South East Polynesia.

Methods

We classified demosponge barcodes using the ribosomal subunit (28S rDNA) of 1,910 sponge samples into molecular operational taxonomic units (MOTUs). MOTU composition of the 13 marine provinces was compared based on Jaccard and Sørenson dissimilarities, and other biodiversity indices.

Results

Our data corroborated high levels of endemism among demosponges. Faunal overlaps were revealed between the Red Sea and the Gulf, which displayed relatively small connectivity with other marine provinces of the Western Indian Ocean. In the Western Indian Ocean, we observed a strong faunistic boundary to the Central Indo-Pacific. The Polynesian sponge faunas were comparatively isolated marine provinces of the Central Indo-Pacific.

Main conclusions

Our data corroborate case studies on sponges that generally reject the presence of cosmopolitan or otherwise widespread sponge species, instead revealing high levels of regional endemism. This is consistent with similar observations and hypotheses in other marine invertebrates. Connectivity among Indo-Pacific marine provinces differs for demosponges in many aspects from that of other marine taxa, such as corals and fishes, probably due to their shorter pelagic larval phase.
Phase separation in the putative fractional quantum Hall
A
phases
Authors: Simon Steven H. , Balram Ajit C.
Published: January 2025

We use several techniques to probe the wave functions proposed to describe the A phases by Das, Das, and Mandal [; ; ]. As opposed to representing fractional quantum Hall liquids, we find these wave functions to describe states that clearly display strong phase separation. In the process of exploring these wave functions, we have also constructed several methods for diagnosing phase separation and generating such wave functions numerically. Finally, we uncover a property of entanglement spectra that can be used as a check for the accuracy of numerics.

Published by the American Physical Society
2025
Tomographic constraint on anisotropic cosmic birefringence
Authors: Namikawa Toshiya
Published: January 2025

We constrain anisotropic cosmic birefringence generated at reionization using Planck PR4 polarization data for the first time. Several recent analyses of WMAP and Planck polarization data have found a tantalizing hint of isotropic cosmic birefringence. Ongoing and future cosmic microwave background (CMB) experiments will test isotropic cosmic birefringence by improving the absolute angle calibration and understanding the intrinsic parity-odd power spectrum of the galactic foregrounds. Alternatively, measuring anisotropies in cosmic birefringence and its time evolution is also a key observable to confirm the signal of cosmic birefringence and to investigate its origin. We discuss estimators of anisotropic cosmic birefringence generated at different redshifts. We then estimate anisotropic cosmic birefringence generated at reionization from the PR4 data, showing that the power spectrum is consistent with null. We find that the model proposed by Ferreira is still consistent with the observation. Future full-sky CMB experiments such as LiteBIRD and PICO will help tighten the tomographic constraint to test models of cosmic birefringence.

Published by the American Physical Society
2025
Black-hole cartography
Authors: Dyer Richard , Moore Christopher J.
Published: January 2025

Quasinormal modes (QNMs) are usually characterized by their time dependence, with oscillations at specific frequencies predicted by black hole (BH) perturbation theory. QNMs are routinely identified in the ringdown of numerical relativity waveforms, are widely used in waveform modeling, and underpin key tests of general relativity and of the nature of compact objects—a program sometimes called BH spectroscopy. Perturbation theory also predicts a specific spatial shape for each QNM perturbation. For the Kerr metric, these are the (s=−2) spheroidal harmonics. Spatial information can be extracted from numerical relativity by fitting a feature with known time dependence to all of the spherical harmonic modes, allowing the shape of the feature to be reconstructed—a program initiated here and that we call “BH cartography.” Accurate spatial reconstruction requires fitting to many spherical harmonics and is demonstrated using highly accurate Cauchy-characteristic numerical relativity waveforms. The loudest QNMs are mapped, and their reconstructed shapes are found to match the spheroidal harmonic predictions. The cartographic procedure is also applied to the quadratic QNMs—nonlinear features in the ringdown—and their reconstructed shapes are compared with expectations based on second-order perturbation theory. BH cartography allows us to determine the viewing angles that maximize the amplitude of the quadratic QNMs, an important guide for future searches, and is expected to lead to an improved understanding of nonlinearities in BH ringdown.

Published by the American Physical Society
2025
Leveraging digital transformation to develop a data-driven culture for supply chain resilience: an empirical investigation
Authors: Kokkinou Alinda , Mitas Ondrej , Mandemakers Albert
Published: January 2025

Purpose

Companies rely on supply chain robustness and resilience to maintain their competitive advantage despite disruptions. The study examines how organizations can orchestrate employee empowerment, digital transformation technologies, and trust to develop supply chain robustness and resilience capabilities.

Design/methodology/approach

A cross-sectional survey design is used to test the study hypotheses. Data are collected from international and domestic organizations operating in the Netherlands, Belgium, and Luxemburg using an online survey, and analyzed using Partial Least Squares-Structural Equation Modeling (PLS-SEM).

Findings

Digital transformation tools contribute to supply chain robustness and resilience in different ways. Digital transformation tools and employee empowerment contribute to the development of a data-driven culture and thereby to supply chain robustness. Digital transformation tools also contribute to increased supply chain visibility. This in turns strengthens trust relationships with suppliers, contributing to supply chain resilience.

Originality/value

The study extends dynamic capability theory and organization information processing theory by demonstrating how investments in assets such as digital technologies can contribute to increasing an organization’s information processing capability directly, by building vertical information systems, but also indirectly, by contributing to the development of lateral relations.
Environmental, social and governance investing: systematic literature review using ADO model
Authors: Aggarwal Shalini , Dsouza Suzan , Joshi Mahesh , Antoun Roger , Phan Duc Hong Thi
Published: January 2025

Purpose

This paper systematically analyzes the literature on environmental, social and governance (ESG). It explores the antecedents, decisions and outcomes (ADO) influencing ESG investments; theories used in the literature; publication years, geographical locations and journals of publication of ESG-related articles; notable gaps in research on ESG investments; theoretical and managerial implications and prospective research avenues within the ESG field. All ESG components are interconnected with the United Nations’ Sustainable Development Goals (SDGs).

Design/methodology/approach

The PRISMA framework was employed to screen articles from the Scopus database. A total of 386 articles spanning 2011–2024 were included. The search terms used to screen the articles for inclusion were “sustainable finance,” “ESG,” “environment, social, corporate governance,” “green finance,” “green bond,” “social bond,” “blue bond,” “social finance” and “corporate social responsibility.”

Findings

The findings indicate that organizations utilize green bonds, blue bonds and green loans to mitigate environmental concerns. To address social issues, companies issue social bonds and sustainable bonds and engage in socially responsible investing. To address concerns about corporate governance, companies emphasize corporate social responsibility and intellectual capital.

Practical implications

The findings can be used to inform policymakers on the implementation of comprehensive regulatory frameworks in the realm of ESG. Tax benefits and subsidies should be extended to firms fostering ESG practices.

Originality/value

This study offers a comprehensive synthesis of the ESG literature by examining the ADO framework, which has not been systematically applied to ESG investments before. It integrates diverse components of ESG investments with the United Nations’ SDGs, providing a unique perspective on how these investments align with global sustainability objectives.
Lenient return policies and religiosity: enhancing consumer confidence, well-being and intentions
Authors: Jamil Raja Ahmed , Khan Tariq Iqbal
Published: January 2025

Purpose

The post-pandemic era has shifted most industries, businesses and consumers online, increasing the demand for electronic devices, mainly laptops. Additionally, most non-Western countries inhabit highly religious but cash-strapped individuals, making them a potential market for second-hand laptops. With this in mind, this study aims to explore the effects of lenient return policy (LRP) and religiosity on consumer confidence in retailer (CCR), consumer well-being and purchase intention.

Design/methodology/approach

This paper conducted a between-subjects field experiment comparing two return policy conditions (cash return vs. other return) with a sample of 222 participants. Data were analysed using partial least squares structural equation modelling (PLS-SEM) to test the hypothesised relationships, and multigroup analysis (MGA) was employed to assess the experimental effects based on the return policy conditions. The moderating effects of religiosity were also examined. All analyses were conducted using SmartPLS software.

Findings

The results confirm that an LRP positively predicts consumer confidence in retailer, well-being and purchase intention. Religiosity had a moderating effect on LRP outcomes. Additionally, the experiment confirmed that consumers experienced better well-being and were more likely to purchase if offered full cashback.

Practical implications

Retailers of second-hand shopping products should offer LRP (full cashback) to foster consumer confidence, well-being and purchase intention. Additionally, for highly religious consumers, aligning return policies with religious principles should further enhance consumer well-being and purchase intention.

Originality/value

This study is among the earliest to investigate the impact of LRP on CCR and well-being. Moreover, a novel attempt is made to explore the moderating effects of religiosity on LRP outcomes. Likewise, a field experiment to validate the greater effects of cashback on consumer well-being and purchase intention adds to the novelty of this study.
The interplay of money laundering and terrorism financing in Saudi Arabia: a critical examination
Authors: Alhejaili Mohammad
Published: January 2025

Purpose

This paper aims to critically analyse the evolving anti-money laundering (AML) and counter-terrorism financing (CTF) framework in Saudi Arabia, focusing on the intersection of Shari’ah and international AML standards. The study explores Saudi Arabia’s efforts to combat money laundering (ML) and terrorism financing (TF) within its global engagement, assessing the challenges and opportunities posed by emerging financial technologies and transnational financial crime.

Design/methodology/approach

The research uses a legal doctrinal analysis of Saudi Arabia’s AML/CTF laws, integrating a review of FATF reports, international guidelines and Shari’ah-compliant financial regulations. The study also evaluates Saudi Arabia’s participation in international AML/CTF cooperation efforts, drawing on case studies of the country’s involvement in global initiatives and bilateral agreements. In addition, the research examines policy recommendations and explores the role of new financial technologies, such as cryptocurrencies and blockchain.

Findings

Saudi Arabia has made significant progress in aligning its AML/CTF framework with global standards, particularly following its full membership in the FATF. However, challenges remain, especially in addressing vulnerabilities within non-financial sectors and regulating emerging financial technologies. The study finds that integrating Shari’ah into the country’s AML/CTF system enhances cultural and religious relevance while contributing to global compliance efforts. International cooperation and technology adoption are essential for staying ahead of evolving threats.

Originality/value

This study uniquely examines the interplay between Shari’ah and global AML standards in Saudi Arabia, offering insights into how religious principles coexist with international regulatory requirements. It also addresses the rising challenges of cryptocurrencies and blockchain, providing actionable policy recommendations for policymakers and financial institutions to enhance Saudi Arabia’s AML/CTF efforts. The research highlights Saudi Arabia’s role as a regional leader and global contributor to financial crime prevention.
Navigating the storm: understanding the impact of a COVID-19-induced negative career shock on career success and life satisfaction in China
Authors: Ma Yin , Bennett Dawn , Donald William E.
Published: January 2025

Purpose

Our study aimed to understand how a negative career shock (CS), caused by the COVID-19 pandemic, a global crisis, impacted employees’ career success and life satisfaction in China.

Design/methodology/approach

Employees (n = 737) from industries adversely impacted by COVID-19-related restrictions (e.g. (a) catering, hotel and tourism; (b) construction and real estate; (c) finance; (d) technology; (e) logistics and (f) manufacturing) responded to an online survey on a negative CS, subjective career success, objective career success (OCS), life satisfaction and protean career orientation (PCO).

Findings

A negative CS was negatively associated with OCS and life satisfaction. Subjective and OCS were positively associated with life satisfaction. PCO moderated the association between a negative CS and OCS.

Practical implications

The practical contribution comes from informing strategies for individuals and employers in China to enact when facing future chance events on a national or global scale.

Originality/value

The theoretical contribution of our research comes from advancing the conservation of resources theory by considering the impact of a negative CS as an independent variable and PCO as a moderator on career success and life satisfaction.
Measuring supply chain resilience performance: role of data analytics, collaboration and flexibility
Authors: Singh Rohit Kumar
Published: January 2025

Purpose

The purpose of this study is to examine the impact of data analytics, collaboration and flexibility on supply chain resilience (SCR) performance in the current dynamic global market.

Design/methodology/approach

This study uses a partial least squares modeling approach to analyze the relationships defined in the conceptual model. This data was organized through a survey questionnaire shared with the professionals working in different industries and belonging to supply chain functions. This survey was designed to measure data analytics capability (DAC), supply chain collaboration (SCC), supply chain flexibility (SCF), industry dynamism (INY) and SCRP, consisting of 29 items. This analysis included involved assessing measurement model for reliability and validity and a structural model for hypothesis testing.

Findings

This research empirically examines that collaboration and flexibility are significantly enhanced by advanced DACs, generating superior SCRP. Furthermore, the findings validate that cooperation and adaptability among the supply chain are necessary to reinforce this inherent resilience. The relation of SCC, SCF and the SCRP was significantly moderated with the INY.

Originality/value

This study complements the extant literature by providing empirical evidence of the tangible effects of data analytics on SCR. The study demonstrates the need for the alignment of supply chain strategies with the INY, giving some directions on how businesses can tailor their practices to specific market environments for enhanced resilience.
Racket sociality: investigating intimidation in North India
Authors: Michelutti Lucia
Published: December 2024

This article is an ethnographic investigation into acts of intimidation and threats. Theoretically, it dialogues with ‘racket’ – a key analytical term in the sociology of domination, state‐making, and mafias. The anthropology of power, violence, and crime has paid scant attention to the morphology of threats and the ways interpersonal intimidation intertwines with economic and political forms of coercion. Drawing on ethnographic insights from North India, the article examines the way (criminal) intimidation is normalized, consented to, and socially embedded in everyday life. It shows how racketeering is routinized beyond clandestine organized crime. Ultimately, ‘racket sociality’ is proposed as a new method of ethnographic inquiry into theorizing authority and legitimacy in an age of populist strongmen politics and predatory forms of capitalism.