bluuebunny/crossref_metadata_2025 huggingface dataset:
A simplified co-culture reveals altered cardiotoxic responses to doxorubicin in hPSC-derived cardiomyocytes in the presence of endothelial cells
Authors: Brescia Marcella , Chatrian Andrea , Keselman Paul , Gallant James , Paulsson Elsa Sörman , Mol Mervyn P.H. , Sjögren Rickard , Raymond Karine , Orlova Valeria , Barnes Kalpana , Wales Richard , Austerjost Jonas , Olszowy Michael W. , Mummery Christine L. , van Meer Berend J. , Davis Richard P.
Published: February 2025

Cardiotoxicity is a significant challenge in cancer therapies, particularly with doxorubicin, a widely used anthracycline known for its broad anti-cancer spectrum but life-threatening cardiac side effects. There is a critical need for more predictivein vitromodels to understand doxorubicin-induced cardiotoxicity and patient-specific drug responses. In this study, we used human pluripotent stem cell (hPSC)-derived cardiomyocytes (hPSC-CMs), cardiac fibroblasts (hPSC-cFBs) and endothelial cells (hPSC-ECs) to investigate the cardiotoxic effects of doxorubicin in two-dimensional mono-and multi-cell type cultures. By mimicking the cumulative dose effect seen in patients through repeated doxorubicin treatments and using a machine learning-basedin silicoimage analysis tool, we could precisely quantify caspase 3/7 activity as an early toxicity marker and identify hPSC-CMs in multi-cell type cultures. This innovative approach allowed continuous monitoring of apoptosis from phase-contrast images, revealing that hPSC-ECs showed higher sensitivity to doxorubicin than isogenic hPSC-CMs or hPSC-cFBs and significantly enhanced cardiomyocyte toxicity in co-culture. In contrast, dermal fibroblasts differentiated from the same hPSC line showed no toxic response under the same treatment regimen. These results challenge the conventional focus on cardiomyocytes as the target of drug-induced cardiac damage. Our findings not only highlight the complex interplay among different cardiac cell types in mediating the toxic effects of doxorubicin, but also demonstrate the potential of AI-enabled tools to advance personalized drug screening and safety assessments.
CTP Drives Human CTPS1 Filamentation
Authors: Guo Chen-Jun , Bao Xiaojie , Liu Ji-Long
Published: February 2025

CTP synthase (CTPS) is a key enzyme in de novo CTP synthesis, playing a critical role in nucleotide metabolism and cellular proliferation. Human CTPS1 (hCTPS1), one of the two CTPS isoforms, is essential for immune responses and is highly expressed in proliferating cells, making it a promising therapeutic target for immune-related diseases and cancer. Despite its importance, the regulatory mechanisms governing hCTPS1 activity remain poorly understood. Here, we reveal that CTP, the product of CTPS, acts as a key regulator for hCTPS1 filamentation. Using cryo-electron microscopy (cryo-EM), we resolve the high-resolution structure of CTP-bound hCTPS1 filaments, uncovering the molecular details of CTP binding and its role in filament assembly. Importantly, we demonstrate that CTP generated from the enzymatic reaction does not trigger filament disassembly, suggesting a conserved regulatory pattern. Furthermore, by analyzing the binding modes of two distinct CTP-binding pockets, we provide evidence that this filamentation mechanism is evolutionarily conserved across species, particularly in eukaryotic CTPS. Our findings not only elucidate a novel regulatory mechanism of hCTPS1 activity but also deepen the understanding of how metabolic enzymes utilize filamentation as a conserved strategy for functional regulation. This study opens new avenues for targeting hCTPS1 in therapeutic interventions.
AIRUS: a simple workflow for AI-assisted exploration of scientific data
Authors: Harris Kenneth D
Published: February 2025

The development "reasoning" large language models (LLMs) seems poised to transform data analysis in all fields of science. This note describes a simple, iterative workflow termed AIRUS (AI Research Under Supervision), that allows working scientists, including those who lack extensive AI or programming expertise, to immediately start taking advantage of these capabilities. In the proposed workflow, a researcher uses an LLM to generate hypotheses, produce code, interpret results, and refine its approach in repeated cycles, only intervening when necessary. This can be run by simple cut-and-paste of code and results between web-based LLMs and an online Jupyter notebook. We demonstrate the workflow with two examples: one analysis of synthetic data, and one analysis of data from the International Brain Lab.
Polarization-Sensitive Optical Coherence Tomography Imaging of Posterior Staphyloma Edges in Eyes with High Myopia
Authors: Wu Yijin , Lu Hongshuang , Chen Changyu , Xiong Jianping , Yamanari Masahiro , Takahashi Hiroyuki , Sugisawa Keigo , Okamoto Michiaki , Wang Yining , Wang Ziye , Takahashi Tomonari , Kamoi Koju , Ohno-Matsui Kyoko
Published: February 2025

Purpose

To investigate the arrangement and orientation of the collagen fibers in the inner and outer scleral layers at the edges of posterior staphylomas using polarization-sensitive optical coherence tomography (PS-OCT).

Methods

195 eyes of 105 highly myopic patients who underwent PS-OCT examinations between August 2023 and May 2024 at Institute of Science Tokyo were studied. The PS-OCT images were analyzed to assess the orientation and birefringence of scleral collagen fibers at the staphyloma edges, covering macular and inferior staphylomas.

Results

Eighty-eight eyes of 60 highly myopic patients whose posterior staphylomas were confirmed in the ultra-widefield optical coherence tomography images underwent PS-OCT image processing. Thirty-six eyes from 27 patients were selected for further analysis. The optic axis images showed that 25 (18 upper and 7 lower) of 30 (83.3%) macular staphyloma edges had an aggregation of the inner scleral fibers, characterized by an arc-like gathering of the horizontal fibers along the edge. All eight upper edges from 8 eyes with an inferior staphyloma had an aggregation of the inner scleral fibers with relatively linear horizontal fibers across the macula. The birefringence images of the upper and lower edges of the macular and inferior staphylomas had different patterns, including a mixture of low and high, and relatively high birefringence.

Conclusions

An uneven aggregation of inner scleral fibers at the staphyloma edges in highly myopic eyes offers a more nuanced understanding of the pathogenesis of staphylomas. This finding also has pivotal implications for developing the targeted interventions to prevent the progression of staphylomas in eyes with high myopia.
Sulfinyl Aziridines as Stereoselective Covalent Destabilizing Degraders of the Oncogenic Transcription Factor MYC
Authors: Rosen Hannah T , Li Kelvin , Li Erin L , Currier Brynne , Brittain Scott M , Garcia Francisco J , Beard Diana C , Haenni-Holzinger Sandra , Dovala Dustin , McKenna Jeffrey M , Schirle Markus , Maimone Thomas J , Nomura Daniel K
Published: February 2025

While MYC is a significant oncogenic transcription factor driver of cancer, directly targeting MYC has remained challenging due to its intrinsic disorder and poorly defined structure, deeming it undruggable. Whether transient pockets formed within intrinsically disordered and unstructured regions of proteins can be selectively targeted with small molecules remains an outstanding challenge. Here, we developed a bespoke stereochemically-paired spirocyclic oxindole aziridine covalent library and screened this library for degradation of MYC. Through this screen, we identified a hit covalent ligand KL2-236, bearing a unique sulfinyl aziridine warhead, that engaged MYC in vitro as pure MYC/MAX protein complex and in situ in cancer cells to destabilize MYC, inhibit MYC transcriptional activity and degrade MYC in a proteasome-dependent manner through targeting intrinsically disordered C203 and D205 residues. Notably, this reactivity was most pronounced for specific stereoisomers of KL2-236 with a diastereomer KL4-019 that was largely inactive. Mutagenesis of both C203 and D205 completely attenuated KL2-236-mediated MYC degradation. We have also optimized our initial KL2-236 hit compound to generate a more durable MYC degrader KL4-219A in cancer cells. Our results reveal a novel ligandable site within MYC and indicate that certain intrinsically disordered regions within high-value protein targets, such as MYC, can be interrogated by isomerically unique chiral small molecules, leading to destabilization and degradation.
Pregnancy laboratory test dynamics resemble rejuvenation of some organs and aging of others
Authors: Moran Ron , Pridham Glen , Toledano Yoel , Alon Uri
Published: February 2025

Aging and pregnancy both involve changes in many physiological systems. Some of these changes are similar, leading to suggestions that pregnancy may be a model for aging. Recent studies using DNA methylation clocks showed apparent aging during gestation which resolves postpartum. Since aging and pregnancy are complex, it is important to compare them in terms of many physiological parameters and at many time points. Here, we analyzed cross-sectional data on 62 lab tests at weekly resolution in 300,000 pregnancies and 1.4 million nonpregnant females aged 20-80. We trained a regression model to predict age from lab tests. Apparent age dropped by 8 years in early pregnancy, rose by 30 years towards delivery, and recovered postpartum. Certain systems exhibited "rejuvenation," with opposite trends in pregnancy and aging, including renal, iron, and most liver tests. Others, such as coagulation, thyroid, muscle, and metabolic systems, showed apparent aging. Some systems displayed mixed trends. Notably, in the systems that showed apparent aging, the physiological mechanisms for the changes differed between pregnancy and aging. Pregnancy complications led to an additional apparent aging of 4-8 years. We conclude that pregnancy is a superficial model of aging that involves different mechanisms and rejuvenation or aging-like changes in different systems. Nevertheless, apparent age may be a convenient way to measure magnitude and direction of physiological perturbations.
Effects of an early water, sanitation, hygiene, and nutritional intervention on child development at school age: a 7-year follow-up of a cluster-randomized trial in rural Bangladesh
Authors: Tofail Fahmida , Pitchik Helen O. , Islam Mahfuza , Khan Rizwana , Shoab Abul K. , Akter Fahmida , Aktar Shirina , Huda Tarique M.N. , Rahman Mahbubur , Winch Peter J. , Luby Stephen P. , Fernald Lia C.H.
Published: February 2025

Background

A previous cluster-randomized controlled trial in Bangladesh found that individual or combined water, handwashing, sanitation, and nutrition interventions during pregnancy and after birth improved developmental outcomes of children at 1 and 2 years of age. We aimed to determine if these intervention effects were sustained at school-age.

Methods and Findings

Pregnant women were enrolled between May 2012 and July 2013 and randomized into chlorinated drinking water (W); improved sanitation (S); handwashing with soap (H); combined WSH; nutrition counselling and provision of lipid-based supplements (N); combined WSH+N, or a passive control arm (C) (N=5,551). We followed-up enrolled mothers and children 5 years after intervention completion. Primary outcomes were child cognition, fine motor abilities, behaviour, school achievement, and executive function; secondary outcomes were maternal mental health and the home environment. We conducted intention to treat analyses using generalized linear models to determine unadjusted and adjusted comparisons between each arm and the control, accounting for pair-matching and block level clustering.

Between September 2019 and February 2021, we re-enrolled 3,832 children. Children in the WSH+N, N, and S arms had improved cognitive scores on one or more domains compared to the control arm, with adjusted effect sizes between 0.10 (95%CI: 0.00, 0.20) and 0.15 (0.03, 0.27). Children in all arms except S had improved prosocial behaviour, with effect sizes between 0.21 (0.07, 0.34) and 0.33 (0.17, 0.49). No intervention effects were observed for fine motor, difficult behaviours, executive functioning, or school achievement. Maternal depressive symptoms were improved in the WSH+N, H, and N arms, and the stimulating home environment was improved in all intervention arms. Data collection for this study was interrupted by a 6-month pause at the start of the COVID-19 pandemic.

Conclusions

At 7 years of age, we found small, sustained impacts of early water, sanitation, hygiene, and nutrition interventions on child cognitive and social-emotional outcomes, the stimulating home environment, and maternal mental health. Future work to determine the mechanisms underlying these intervention effects will further inform the design of early interventions to improve child health and development.

Trial registration

Follow-up trial:ClinicalTrials.gov,NCT04443855

Original WASH-Benefits Bangladesh (WASH-B):ClinicalTrials.gov,NCT01590095
Women's Empowerment and Quality Antenatal Care in Ghana: Analysis of the SWPER Global Index in the Ghana Demographic Health Survey.
Authors: Bessing Barnabas , Koray Munawar Harun , Baatiema Linus
Published: February 2025

Background: Women's empowerment is a key determinant of maternal healthcare utilization, influencing antenatal care (ANC) quality in low- and middle-income countries (LMICs). While ANC is crucial for maternal and neonatal health outcomes, disparities persist in service uptake and quality in Ghana. This study examines the association between women's empowerment, measured using the Survey-based Women’s emPowERment (SWPER) index, and the receipt of quality ANC in Ghana. Methods: A cross-sectional analysis was conducted using the 2022 Ghana Demographic and Health Survey (GDHS) data. The study included 8,715 women aged 15–49 who attended ANC during pregnancy. Quality ANC received four essential services: blood pressure monitoring, urine testing, iron supplementation, and blood sample collection. Women’s empowerment was assessed across three SWPER domains: attitude toward violence, decision-making, and social independence, categorised into low, medium, and high levels. Logistic regression models examined the relationship between empowerment and quality ANC while adjusting for demographic and socioeconomic variables. Results: The study found that 95% of women received quality ANC services despite significant disparities across demographic and socioeconomic groups. Higher levels of women's empowerment were positively associated with quality ANC. Specifically, women with high empowerment in attitude toward violence (AOR: 1.92; 95% CI: 1.53 - 3.10), social independence (AOR: 1.82; 95% CI: 1.69 - 1.99), and decision-making (AOR: 1.31; 95% CI: 1.09 - 1.58) were significantly more likely to receive quality ANC than their low-empowerment counterparts. Other significant predictors of quality ANC included higher education, wealth index, older maternal age, urban residence, and media exposure. Women in rural areas and those in the Northern, Northeast, and Savannah regions were significantly less likely to receive quality ANC. Conclusion: Women's empowerment is a key driver of quality ANC utilisation in Ghana. Strengthening empowerment initiatives such as increasing educational opportunities, enhancing economic autonomy, and promoting decision-making power can improve maternal health outcomes. Addressing regional disparities and integrating empowerment strategies into maternal health policies can enhance ANC quality and reduce maternal and neonatal mortality in Ghana.
Life Course Sleep Duration Trajectories and Risk and Age at Onset of Parkinson’s Disease
Authors: Fang Yi , Hardy Rebecca , Yaffe Kristine , Little Simon J. , Tanner Caroline M. , Leng Yue
Published: February 2025

Importance

Investigating associations between life course sleep duration and Parkinson’s disease (PD) may help clarify the role of sleep in early detection and/or prevention of PD.

Objective

To characterize life course sleep duration trajectories and their associations with PD risk and age at onset (AAO).

Design

Two ongoing online cohorts: Parkinson’s Progression Markers Initiative (PPMI)-Online (discovery; started in 2021) and Fox Insight (FI; validation; started in 2018).

Setting

Participants reported sleep duration across life stages, with PD-related follow-ups every three months.

Participants

A convenience sample of 5,660 individuals with PD and 10,245 without PD from PPMI-Online, and 1,929 participants with PD from FI.

Exposures

Self-reported sleep duration from ages 18 to 80+ in PPMI-Online and 12 to 66+ in FI. Latent class growth analysis (LCGA) identified sleep trajectories.

Main Outcomes and Measures

PD risk and AAO were assessed using logistic and linear regression, adjusting for demographics, lifestyle, comorbidities.

Results

The combined sample included 17,834 participants [age at sleep report 67.2±7.83 years; 9,735 (54.6%) female]. LCGA identified nine sleep trajectories in PPMI-Online, stable in early adulthood but diverging in midlife (stable, increasing, decreasing). Midlife sleep reductions (6-7 to ≤5-6 hours/day: OR = 1.90, 95% CI 1.61-2.24,P< .001; 7-8 to ≤6-7 hours/day: OR = 1.64, 95% CI 1.40-1.91,P< .001) and consistent short sleep (<=6 hours/day throughout adulthood: OR = 1.41, 95% CI 1.19-1.67, P < .001) demonstrated increased PD risk. Short sleep in early adulthood or midlife also had earlier AAO. The strongest effects were seen in those with ≤6 hours/day throughout adulthood (PPMI-Online: β = −2.45 years, 95% CI −3.33 to −1.56, P <.001) and those with a continuous decrease since adolescence (FI: β = −4.23 years, 95% CI −5.52 to −2.93, P < .001). These effects were independent of rapid eye movement sleep behavior disorders.

Conclusions and Relevance

Self-reported short sleep in early adulthood and midlife sleep reductions are associated with increased PD risk and earlier AAO. Self-perceived midlife sleep reduction may be a marker for future PD. Persons with chronic short sleep may be candidates for preventive intervention.

Key Points

Question:What is the relationship between life course sleep duration trajectories and the risk and age at onset of Parkinson’s disease (PD)?

Findings:In this cohort study including 7,589 participants with PD and 10,245 without PD, short sleep duration in early adulthood or decreasing sleep duration after age 50 were associated with an increased risk and earlier age at onset of PD.

Meaning:Short sleep duration over the life course, even in early adulthood (< 40 years), may contribute to risk of late-life PD; declining sleep duration after age 50 is a potential prodromal sign of PD.
Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring
Authors: Sugimoto Hikaru , Sapir Gal , Keshet Ayya , Kuroda Shinya
Published: February 2025

An unmet need for preventing diabetes complications is the early detection of metabolic dysregulation. While glucose dynamics provide high-dimensional insights into metabolic states, extracting comprehensive and interpretable information from such data remains challenging. Here we show that the majority of inter-individual variation in glucose dynamics can be captured by just three features - mean, variance and autocorrelation - each independently associated with diabetes-related measures, even in individuals without a prior diabetes diagnosis. Analysis of continuous glucose monitoring data from 8,025 individuals showed that these three measures explained over 80% of the inter-individual variation in glucose dynamics. These measures outperformed conventional measures, including fasting, mean, and 2-hour postprandial glucose levels, in reconstructing postprandial glucose dynamics. Each feature showed independent associations with vascular or hepatic status. By condensing high-dimensional glucose dynamics into three interpretable features with minimal loss of information, this framework provides a basis for a more accurate diabetes risk assessment.
A Scalable Method for Validated Data Extraction from Electronic Health Records with Large Language Models
Authors: Stuhlmiller Timothy J. , Rabe AJ , Rapp Jeff , Manasco Penelope , Awawda Alaa , Kouser Hiba , Salamon Hugh , Chuyka Donald , Mahoney William , Wong Kenny K. , Kramer Glenn A. , Shapiro Mark A.
Published: February 2025

Purpose

Extracting and structuring relevant clinical information from electronic health records (EHRs) remains a challenge due to the heterogeneity of systems, documents, and documentation practices. Large Language Models (LLMs) provide an approach to processing semi-structured and unstructured EHR data, enabling classification, extraction, and standardization.

Methods

Medical documents are processed through a structured data pipeline to generate normalized FHIR data. Unstructured data undergoes preprocessing, including optical character recognition, document parsing, text chunking and embedding. Embedding enables search and classification which facilitate document retrieval for extraction. LLMs perform named entity recognition and relation extraction, with outputs mapped to FHIR R4 and OMOP and harmonized with pre-structured data for interoperability. Model performance is evaluated through human validation and automated consistency checks. Iterative refinement, error analysis, and standardized schema selection optimize use for analytics and downstream workflows.

Results

An LLM-based schema for medication extraction, validated on 34 patients, achieved ∼95% accuracy and F1-score across 7 data fields for 5,789 extracted medications. Deployment across 11,115 patients extracted 2.6 million medication records, increasing total medications by 27% and distinct drug ingredients by 31% over structured data in the EHR. LLM extraction increased oncology medications by 60%, distinct oncology therapies by 64%, and the number of patients with structured oncology medication data by 33%. The LLM enhanced data completeness, improving availability of indication for prescription (61% vs. 31%) and discontinuation reason (17% vs. 0%), outperforming pre-structured data in key clinical variables.

Conclusion

An LLM-powered extraction process that employs embeddings, machine learning classification, schema-based extraction, and mapping of extracted information to healthcare data standards, achieves a significant gain in clinically relevant information over pre-structured data available in the EHR.
Cryo-EM structures of the Plant Augmin reveal its intertwined coiled-coil assembly, antiparallel dimerization and NEDD1 binding mechanisms
Authors: ashaduzzaman MD , Taheri Aryan , Lee Yuh-Ru Julie , Tang Yuqi , Guo Fei , Fried Stephen D. , Liu Bo , Al-Bassam Jawdat
Published: February 2025

Microtubule (MT) branch nucleation is fundamental for building parallel MT networks in eukaryotic cells. In plants and metazoans, MT branch nucleation requires Augmin and NEDD1 proteins which bind along MTs and then recruit and activate the gamma-tubulin ring complex (γ-TuRC). Augmin is a fork-shaped assembly composed of eight coiled-coil subunits, while NEDD1 is a WD40 β-propellor protein that bridges across MTs, Augmin, and γ-TuRC during MT branch nucleation. Here, we reconstitute hetero-tetrameric and hetero-octameric Arabidopsis thaliana Augmin assemblies, resolve their subunit interactions using crosslinking mass spectrometry and determine 3.7 to 7.3-Å cryo-EM structures for the V-junction and extended regions of Augmin. These structures allowed us to generate a complete de novo plant Augmin model that reveals the long-range multi coiled-coil interfaces that stabilize its 40-nm hetero-octameric fork-shaped organization. We discovered the dual calponin homology (CH) domain forming its MT binding site at the end of its V-junction undertake open and closed conformations. We determined a 12-Å dimeric Augmin cryo-EM structure revealing Augmin undergoes anti-parallel dimerization through two conserved surfaces along the Augmin extended region. We reconstituted the NEDD1 WD40 β-propellor with Augmin revealing it directly binds on top its V-junction and enhances Augmin dimerization. Our studies suggest that cooperativity between the Augmin dual CH domains and NEDD1 binding site may regulate Augmin V-junction dual binding to MT lattices. This unique V-shaped dual binding and organization anchors Augmins along MTs generating a platform to recruit γ-TuRC and activate branched MT nucleation.
Virus-host interactome reveals host cellular pathways perturbed by tick-borne encephalitis virus infection
Authors: Sui Liyan , Zhao Yinghua , Wang Heming , Chi Yinghua , Xie Hanxi , Tian Tian , Wang Wenfang , Zhu Mucuo , Zhai Naicui , Song Zhixia , Xu Yueshan , Zhang Kaiyu , Che Lihe , Wang Guoqing , Liu Nan , Zhao Yicheng , Liu Quan
Published: February 2025

Tick-borne encephalitis virus (TBEV) poses an increasingly significant threat to public health. Here, we delved into the virus-host interactome and discovered that TBEV has a profound impact on multiple host cellular pathways. Viral pre-membrane protein (prM), non-structural proteins NS1, NS2B3, NS4A, and NS5 remodel the host's innate immune responses. PrM and NS2B3 are involved in autophagy, NS4A is associated with neurodegenerative diseases, and NS5 participates in spliceosome dynamics, ribosomal biogenesis, cell cycle regulation, and DNA damage response. Notably, TBEV infection causes G0/G1 cell cycle arrest in host cells. NS5 interacts with histone acetyltransferase P300 to upregulate P16 expression, suppressing CDK4 and resulting in cell cycle arrest. Elevated P16 and reduced CDK4 levels were observed in TBEV-infected brain organoids. The P300 inhibitors and CDK4 agonist can reverse virus-induced cell cycle arrest and inhibit viral replication. Further analysis uncovered potential antiviral targets like KAT6A, XIAP, and RIOK1/BRD9. These findings provide valuable insights into TBEV pathogenicity and hold promise for antiviral drug development.
Compost amendments to potato soils enrich yield-associated members of soil microbiomes across the continental US
Authors: Klasek Scott A. , Crants James E. , Frost Kenneth E. , Schroeder Brenda K. , Rosen Carl J. , Kinkel Linda L.
Published: February 2025

Plant health is regulated by complex consortia of soil microbes with growth-promoting and pathogenic functions. In potato production, various soil management practices are undertaken to boost yields and suppress diseases, but connections between these practices, soil microbiomes, and tuber yields have not been characterized across diverse growing regions. To identify growing practices and microbes associated with increased yields, we established four-year field trials across eight US sites from Oregon to Maine that consisted of controls, fumigations, organic amendments, and mustard incorporations. Soil microbiomes consisted of 16S and ITS amplicon sequences from bacteria and microeukaryotes, respectively. While soil treatments influenced microbiomes differently across all field sites, eukaryotes were more sensitive than bacteria to all treatments. Soil treatments impacted proportions of distinct amplicon sequence variants (ASVs), and associations between ASVs and tuber yields varied within genus-level taxonomy and across field sites. Forty-five ASVs were identified as both treatment-impacted and yield-associated within any field site. Models identified three of thirteen compost amendment scenarios and one of thirteen fumigation scenarios that increased tuber yields by increasing proportions of these taxa within soil microbiomes. These ASVs were not influenced by treatment-associated changes in soil nutrients or organic matter, highlighting complex relationships within specific field sites that require further study to achieve the goal of implementing sustainable, microbiome-informed potato production techniques.

Importance

Soil microbes play diverse and interconnected roles in mediating plant health, growth, and disease, but understanding the specifics of how they work and applying them across different agricultural systems remains a challenge. To address this, we amassed a dataset from eight potato field sites across major US growing regions consisting of nearly two thousand soil bacterial and fungal microbiomes paired with soil chemical and tuber yield data. We describe how soil microbiomes are impacted by different soil treatments (compost amendments, chemical fumigation, and mustard incorporation), and identify treatments that boosted yields by up to 23% by increasing proportions of certain bacterial or fungal sequences. Compost amendments affected yield-associated taxa more often than other soil treatments, but these effects varied by rotation length and growing region. Changes to soil chemistry resulting from specific soil treatments did not influence abundances of yield-associated taxa, suggesting that the ways in which they may act to maintain plant vigor are field-specific and complex, calling for further study.
A Novel mTOR-Stat3-Stathmin Pathway Establishes Oocyte Polarization Competence by Orchestrating Centrosome Regulation and Microtubule Organization
Authors: Shawahny Amal , Bogoch Yoel , Elkouby Yaniv M
Published: February 2025

In animals and plants, egg production is essential for fertility, reproduction, and embryonic development. The production of functional eggs in sufficient numbers for a female lifespan requires dynamic and precisely coordinated cellular and developmental programs in early oogenesis. However, our understanding of their underlying regulatory mechanisms is critically lacking. Here, we aimed to identify overlooked essential regulators of early oogenesis in zebrafish. First, we present the establishment of a long-term ovary culture system which enables physiological oocyte development from oogonia to primordial follicles in cultured ovaries, providing an invaluable ex-vivo platform for rapid investigation. Next, we utilized this system for robust functional screening of candidates from stage-specific oocyte transcriptomic data. We identified mTOR, Stat3, and Stathmin as novel regulators of oocyte polarity. By using a combination of genetics, pharmacological manipulations ex-vivo, and rescue experiments, we established an essential mTOR-Stat3-Stathmin pathway that orchestrates centrosome regulation and microtubule organization to facilitate oocyte polarity. Microtubules control the localization and condensation of the essential polarity regulator Bucky ball (Buc). Loss of mTOR or Stat3 functions, as well as overactivation of Stathmin (a microtubule destabilizing protein) resulted in aberrant centrosome regulation and destabilization of microtubules, leading to dispersed mis-localized Buc condensates and loss of polarity. We show that mTOR acts upstream of Stat3 in oocytes, and that inhibition of Stathmin in stat3-/- or mTOR deficient ovaries rescued both cytoskeletal and polarity defects. We propose a novel mTOR-Stat3-Stathmin pathway which through cytoskeletal regulation, provides oocytes with polarization competence, a step likely widely conserved in biology. mTOR, Stat3, and Stathmin are known for their roles in cellular growth and cancer. Our work reveals their novel unpredicted functions in cell polarity during animal post-embryonic development.
Quantum chromodynamics resolution of the ATOMKI anomaly in
He4
nuclear transitions
Authors: Kubarovsky Valery , West Jennifer Rittenhouse , Brodsky Stanley J.
Published: February 2025

Observations of anomalous angular correlations in electron-positron pairs produced from excited states of He4, Be8, and C12 nuclei have been suggested as being due to the creation and subsequent decay of a new light particle of mass ∼17MeV. In this work, we investigate the possibility that the source of the observed signals is a set of new excitation channels created by the 12-quark hidden-color Fock state within the He4 nuclear wave function dubbed the “hexadiquark.” We calculate the invariant e+e− mass spectrum for the electromagnetic transition from a new excitation of He4, estimating its differential and total decay width. We find that we can fit the shape of the anomalous signal with the QCD Fock state at excitation energy E*=17.9±1MeV and a Gaussian form factor for the electromagnetic decay. We address the physical issues with the fit parameters using properties of the hexadiquark state, in particular the three weakly repulsive 6C interactions of SU(3)C between diquark pairs. Experimental tests of our model are described in detail. In light of this work, we emphasize the need for independent experimental confirmation or refutation of the ATOMKI results as well as dedicated experiments to search for the proposed new excitations of He4 and other α-cluster nuclei.

Published by the American Physical Society
2025
A deployable agile blockchain as a service (aBaaS) framework for construction projects
Authors: Lu Weisheng , Wu Liupengfei , Yang Zhongze , Peng Ziyu , Chu Louis
Published: February 2025

Purpose

This study aims to develop an agile blockchain as a service (aBaaS) framework for construction projects, which will support blockchain design, deployment and operation in a flexible, agile and cost-effective manner.

Design/methodology/approach

This research adopts a design science research method. The aBaaS framework is then substantiated through two case studies pertinent to construction projects.

Findings

It is found to be highly flexible, achieving high completion rates in customizing the design, deployment and visualization of blockchain systems within given periods. Also, the aBaaS framework is highly agile and cost-effective, capable of responding to changes with low person-day units and labor cost.

Research limitations/implications

Limited sub-service components are built in design management as services (DMSs), deployment as services (DESs) and visualization as services (VISs) of aBaaS framework.

Practical implications

This research offers a reference for those aiming to realize the potential of blockchain in construction projects.

Originality/value

Firstly, it introduces a novel, flexible modular-build DMSs method to help system developers design blockchain systems for projects. Secondly, it improves the blockchain deployment methods by offering plug-and-play DESs for projects. Thirdly, it accelerates the visualization processes for blockchain users in projects by offering them flexible, click-to-go and cost-effective VISs.
Identifying the researchable themes in seventh sustainable development goal: affordable and clean energy
Authors: Murad Muhammad , Othman Shahrina Binti , Kamarudin Muhamad Ali Imran Bin
Published: February 2025

Purpose

The purpose of this study is to present a bibliometric analysis of affordable and clean energy research, focusing on key themes, collaboration patterns and the field’s intellectual structure.

Design/methodology/approach

Using a sample of 37 articles from Scopus, the authors identified the most frequently used keywords, the most productive countries and organizations and categorized research themes into niche, motor, basic and emerging or declining themes. “Clean Energy,” “Renewable Energy” and “Affordable and Clean Energy” emerged as dominant keywords, highlighting the field’s alignment with global sustainability goals. The USA, China and India were found to be the most productive countries, while institutions like Sri Manakula Vinayagar Engineering College and Nigerian National Petroleum Company played pivotal roles in collaborative networks, reflecting a globalized and interdisciplinary research environment.

Findings

The thematic analysis revealed that motor themes, such as “Climate Change” and “Greenhouse Gases”, are central to the discourse, while topics like “Economic Development” and “Energy Conservation” were identified as niche areas. Basic themes, including “Carbon Dioxide” and “Electricity Industry,” remain foundational yet underdeveloped.

Originality/value

This study provides a structured overview of the affordable and clean energy research landscape, offering insights into current trends and identifying areas for future exploration, with an emphasis on interdisciplinary collaboration and socio-economic impacts.
Empirical forecasting of housing prices in Malaysia using ARIMA
Authors: Olanrewaju AbdulLateef
Published: February 2025

Purpose

Housing provision is a fundamental driver of national development and economic prosperity. However, housing affordability remains a critical problem worldwide, affecting countries regardless of their level of development, whether developed, developing or underdeveloped. The housing price index (HPI) measures trends in residential property prices and provides valuable insights into market dynamics. This study aims to model and forecast the HPI in Malaysia. Accurate HPI predictions are essential for informing policy decisions, guiding investment strategies and ensuring sustainable housing market development.

Design/methodology/approach

The autoregressive integrated moving average (ARIMA) model was used to analyse historical housing price data for modelling and forecasting housing prices for different types. The accuracy and reliability of the models and forecasts were assessed using key statistical metrics, including variance (s²), log-likelihood, Akaike information criterion, corrected Akaike information criterion and Bayesian information criterion.

Findings

The findings demonstrate that the ARIMA model improves accuracy in capturing seasonal and trend components in the Malaysian housing market, offering actionable insights for strategic decision-making. In addition, this research presents point and annual changes across different housing types that seek to offer a detailed view of price movements. By providing a reliable five-year forecast of the HPI, this study enables more informed decision-making in housing policy, investment strategy and financial planning.

Practical implications

Policymakers can use these insights to stabilise housing markets, whereas investors and developers can anticipate market movements for better capital allocation. Homeowners and prospective buyers will benefit from understanding future price trends, allowing for more strategic decisions regarding property purchases or sales.

Originality/value

The originality of the study lies in its ability to empirically forecast housing prices for various types of housing for the next five years. This provides valuable guidance for housing-related decisions. This research contributes to the growing literature on real estate forecasting in emerging markets and underscores the relevance of advanced time series models in navigating the complexities of dynamic housing markets.
The impact of forced electricity rationing on shopping and media consumption
Authors: Lappeman James , Dlamini Siphiwe , Zulu Ntsatsi , Wahl Kathryn , Cheteni Priviledge
Published: February 2025

Purpose

This study provides detailed insights into how electricity rationing affects shopping and media consumption in an emerging market context. Given that electricity rationing (also known as load-shedding) is a regular occurrence in many countries, this research brings a unique consumer perspective.

Design/methodology/approach

The study employed a qualitative exploratory design to investigate the effect of electricity rationing on shopping and media consumption. A combined convenience and snowball sampling technique was utilised to select 78 households across various locations in South Africa. Through in-depth interviews and thematic analysis, themes were extracted and explained.

Findings

The findings showed that, for higher-income households, media consumption remained relatively consistent or increased during load-shedding periods. Middle-income families showed a mixed pattern of media use in response to load-shedding. Lower-income households were found to bear the brunt of media-consumption constraints caused by electricity shortages. Consumers are increasingly switching to streaming alternatives to adapt to the limitations of load-shedding. The availability of streaming platforms on mobile devices and laptops and limited household battery backups allows viewers to sidestep disruptions caused by outages.

Originality/value

While electricity outages are the norm in many countries, the impact on shopping and media consumption is significant. To date, no other research has comprehensively explored the impact of these outages on consumer behaviour in emerging markets.
Is university teaching aligned with the sustainable development goals possible? An approach through the virtual training of university professors
Authors: Espejo-Antúnez Luis , Corrales-Serrano Mario , Zamora-Polo Francisco , Cardero-Durán María de los Ángeles
Published: February 2025

Purpose

This study aims to determine the degree of knowledge acquired by university professors after receiving virtual training on the sustainable development goals (SDGs) and their relationship with the contents of the subjects taught.

Design/methodology/approach

A 40-h virtual course on SGDs and higher education was designed. To evaluate professor knowledge, a questionnaire was administered to professors from different fields of knowledge. The questionnaire consists of 25 questions divided into two sections: Section 1: Q1–Q8 (knowledge and access to information) and Section 2: Q9–Q25 (the relationship of the subjects taught with the 17 SDGs). The virtual classroom was used to do the questionnaire and it lasted 10 min. The internal consistency of the different constructs was analyzed by Cronbach’s alpha, Kaiser–Meyer–Olkim test and Marlett test. Descriptive and inferential analysis were also performed.

Findings

Statistical analysis showed a high reliability for the constructs (smallest Cronbach’s alpha = 0.908). Virtual teaching to teachers significantly improves the results of Section 1 (Q1–Q8) (p < 0.001) and Section 2 (Q9–Q25) (p < 0.001) of the questionnaire. Teachers aged 40–50 years significantly associate the contents of their subjects with SDG1 (Q9, p = 0.02), SDG2 (Q10, p = 0.00) and SDG8 (Q16, p = 0.04) previous course. In addition, the area of origin may influence knowledge about the SDGs. At the end of the course, there were no significant differences between teachers by age, field of knowledge or academic category.

Originality/value

Virtual training on SDGs unifies the knowledge of university faculty, promoting academic curricula aligned to sustain-able training, regardless of age, gender, academic category or field of knowledge.
Multiscale damage analysis of engineering structures from material level to structural level: a systematic review
Authors: Liu Yawen , Sun Bin , Guo Tong , Li Zhaoxia
Published: February 2025

Purpose

Damage of engineering structures is a nonlinear evolutionary process that spans across both material and structural levels, from mesoscale to macroscale. This paper aims to provide a comprehensive review of damage analysis methods at both the material and structural levels.

Design/methodology/approach

This study provides an overview of multiscale damage analysis of engineering structures, including its definition and significance. Current status of damage analysis at both material and structural levels is investigated, by reviewing damage models and prediction methods from single-scale to multiscale perspectives. The discussion of prediction methods includes both model-based simulation approaches and data-driven techniques, emphasizing their roles and applications. Finally, summarize the main findings and discuss potential future research directions in this field.

Findings

In the material level, damage research primarily focuses on the degradation of material properties at the macroscale using continuum damage mechanics (CDM). In contrast, at the mesoscale, damage research involves analyzing material behavior in the meso-structural domain, focusing on defects like microcracks and void growth. In structural-level damage analysis, the macroscale is typically divided into component and structural scales. The component scale examines damage progression in individual structural elements, such as beams and columns, often using detailed finite element or mesoscale models. The structural scale evaluates the global behavior of the entire structure, typically using simplified models like beam or shell elements.

Originality/value

To achieve realistic simulations, it is essential to include as many mesoscale details as possible. However, this results in significant computational demands. To balance accuracy and efficiency, multiscale methods are employed. These methods are categorized into hierarchical approaches, where different scales are processed sequentially, and concurrent approaches, where multiple scales are solved simultaneously to capture complex interactions across scales.
Nexus between competition, concentration and bank risk-taking in Indonesian Islamic banking
Authors: Widarjono Agus , Alam Md. Mahmudul , Rafik Abdur , Afandi Akhsyim , Sidiq Sahabudin
Published: February 2025

Purpose

This study aims to investigate the relationship between competition and bank risk-taking in Indonesian Islamic banking using linear and non-linear approaches.

Design/methodology/approach

The dynamic panel regression using a two-step system generalized method of moments (GMM) is used to investigate the impact of competition on Z-score and financing loss provision (FLP) as proxies of bank stability and financing risk, respectively. This study uses all Indonesian Islamic banks (IB) from 2015–2020 using quarterly data.

Findings

The competition positively affects the Z-score and negatively influences the FLP. Furthermore, higher concentration is positively linked to the Z-score but is negatively related to the FLP. This study also incorporates a quadratic term of the competition to examine the competition-stability nexus. The findings indicate that the squared competition is negative for the Z-score and positive for the FLP. In general, this study confirms the competition-stability view.

Research limitations/implications

Some policy implications can be drawn from this study. Indonesia needs more players, and they are large IB in the form of full-fledged IB. This research uses all IB in Indonesia, but these results reflect conditions in one country with its own business and political environments. Of course, the findings cannot be generalized for all IB worldwide using cross-country data.

Originality/value

To the best of the authors’ knowledge, this is the first study that examines the non-linear relationship between competition and stability using the adjusted Lerner index in IB.