bluuebunny/crossref_metadata_2025 huggingface dataset:
A multimodal neuroimaging study of cerebrovascular regulation: protocols and insights of combining electroencephalography, functional near-infrared spectroscopy, transcranial Doppler ultrasound, and physiological parameters
Authors: Burma Joel S , Johnson Nathan E , Oni Ibukunoluwa K , Lapointe Andrew P , Debert Chantel T , Schneider Kathryn J , Dunn Jeff F , Smirl Jonathan D
Published: January 2025

Objective. The current paper describes the creation of a simultaneous trimodal neuroimaging protocol. The authors detail their methodological design for a subsequent large-scale study, demonstrate the ability to obtain the expected physiologically induced responses across cerebrovascular domains, and describe the pitfalls experienced when developing this approach. Approach. Electroencephalography (EEG), functional near-infrared spectroscopy (fNIRS), and transcranial Doppler ultrasound (TCD) were combined to provide an assessment of neuronal activity, microvascular oxygenation, and upstream artery velocity, respectively. Real-time blood pressure, capnography, and heart rate were quantified to control for the known confounding influence of cardiorespiratory variables. The EEG-fNIRS-TCD protocol was attached to a 21 year-old male who completed neurovascular coupling/functional hyperemia (finger tapping and ‘Where’s Waldo/Wally?’), dynamic cerebral autoregulation (squat-stand maneuvers), and cerebrovascular reactivity tasks (end-tidal clamping during hypocapnia/hypercapnia). Main results. In a pilot participant, the Waldo task produced robust hemodynamic responses within the occipital microvasculature and the posterior cerebral artery. A ∼90% decrease in alpha band power was seen in the occipital cortical region compared between the eyes closed and eyes opened protocol, compared to the frontal, central, and parietal regions (∼80% reduction). A modest increase in motor oxygenated hemoglobin was seen during the finger tapping task, with a harmonious alpha decrease of ∼15% across all cortical regions. No change in the middle or posterior cerebral arteries were noted during finger tapping. During cerebral autoregulatory challenges, sinusoidal oscillations were produced in hemodynamics at 0.05 and 0.10 Hz, while a decrease and increase in TCD and fNIRS metrics were elicited during hypocapnia and hypercapnia protocols, respectively. Significance. All neuroimaging modalities have their inherent limitations; however, these can be minimized by employing multimodal neuroimaging approaches. This EEG-fNIRS-TCD protocol enables a comprehensive assessment of cerebrovascular regulation across the association between electrical activity and cerebral hemodynamics during tasks with a mild degree of body and/or head movement.
Response of a tenomodulin-positive subpopulation of human adipose-derived stem cells to decellularized tendon slices
Authors: Li Xuan , Cui Jing , Ning Liang-Ju , Hu Ruo-Nan , Zhao Lei-Lei , Luo Jia-Jiao , Xie Xin-Yue , Zhang Yan-Jing , Luo Jing-Cong , Li Zheng-Yong , Qin Ting-Wu
Published: January 2025

The selection of appropriate cell sources is vital for the regeneration and repair of tendons using stem cell-based approaches. Human adipose-derived stem cells (hADSCs) have emerged as a promising therapeutic strategy for tendon injuries. However, the heterogeneity of hADSCs can lead to inconsistent or suboptimal therapeutic outcomes. In this study, we isolated and identified a tenomodulin (TNMD)-positive subpopulation from hADSCs (TNMD+ hADSCs) using flow cytometry and then assessed the cellular response of this subpopulation to decellularized tendon slices (DTSs), including cell proliferation, migration, and tenogenic differentiation, using the CCK-8 assay, transwell migration assay, and quantitative real-time polymerase chain reaction. Our findings revealed that TNMD+ hADSCs maintained the general characteristics of stem cells and exhibited significantly higher expressions of tendon-related markers compared to hADSCs. Importantly, DTSs significantly enhanced the proliferation, migration, and tenogenic differentiation of TNMD+ hADSCs. This study provides preliminary experimental evidence for the translational application of ADSCs for tendon regeneration and repair.
Achieving 32.9% efficiency in Pb-Based quantum dot solar cells via SCAPS-1D simulation optimization
Authors: Hasnain Md , Wahed Abdul , Das Joyonta , Arkook Bassim , Harb Moussab , Mia Nasim
Published: January 2025

This study presents a comprehensive investigation and in-depth analysis of the optimization of Pb-based quantum dot solar cells (QDSCs), concentrating on the influences of doping concentration, absorber layer thickness, defect density, temperature, and resistive elements. We systematically examined three absorber materials: lead sulfide (PbS), tetrabutylammonium iodide-treated PbS (PbS-TBAI), and lead selenide (PbSe) quantum dots (QDs). Optimal doping concentrations of

1
×

10

17

cm−3 for PbS and

1
×

10

22

cm−3 for both PbS-TBAI and PbSe were identified. Our findings reveal that precise control of these parameters can significantly enhance power conversion efficiency (PCE), achieving values of 24.6%, 28%, and 26.2% for PbS, PbS-TBAI, and PbSe, respectively. Additionally, we investigated the impact of absorber layer thickness on device performance. We discovered that a 1 µm thickness for PbS yields a maximum PCE of 32.9% due to balanced photon absorption and reduced Shockley–Read–Hall recombination. Conversely, PbSe’s performance declined with increased thickness because of its layer-dependent bandgap. We found that lower defect densities (

1
×

10

14

cm−3) critically improve PCE and fill factor across all materials. The temperature-dependent studies demonstrated that PbS-TBAI exhibits remarkable resilience, maintaining efficiency under thermal stress due to effective surface passivation. Analyses of series and shunt resistances highlighted the importance of minimizing internal resistances to optimize device performance. The proposed device structure comprises a fluorine-doped tin oxide front contact layer, a silver sulfide (Ag2S) electron transport layer, the QD absorber layer (PbS, PbS-TBAI, or PbSe), and copper(I) oxide (Cu2O) hole transport layer. Utilizing cascade band alignment, we achieved a record PCE of 32.9%. This research highlights the significant potential of Pb-based QDSCs for achieving high efficiencies through promising material and structural optimization, positioning them as competitive candidates for next-generation solar technologies. The results provide a valuable understanding of designing high-performance QDSCs, paving the way for their integration into sustainable energy solutions.
Searching for (sharp) thresholds in random structures: Where are we now?
Authors: Perkins Will
Published: January 2025

We survey the current state of affairs in the study of thresholds and sharp thresholds in random structures on the occasion of the recent proof of the Kahn–Kalai conjecture by Park and Pham and the fairly recent proof of the satisfiability conjecture for large

k
k

by Ding, Sly, and Sun. Random discrete structures appear as fundamental objects of study in many scientific and mathematical fields including statistical physics, combinatorics, algorithms and complexity, social choice theory, coding theory, and statistics. While the models and properties of interest in these fields vary widely, much progress has been made through the development of general tools applicable to large families of models and properties all at once. Historically, these tools originated to solve or make progress on specific difficult conjectures in the areas mentioned above. We will survey recent progress on some of these hard problems and describe some challenges for the future.

This survey was prepared in conjunction with a talk for the Current Events Bulletin at the 2024 Joint Mathematics Meetings (JMM) in San Francisco, California.
Macroevolutionary and biomechanical implications of rostral flexion in bat skulls: a major early driver of cranial evolution in bats
Authors: Gilley Delaney T , Santana Sharlene E , Arbour Jessica H
Published: January 2025

The evolution of unique morphological features can significantly constrain the subsequent phenotypic diversification of a clade. Bats show diverse skull shapes and are salient among mammals in their dramatic reorientation of major cranial features due to changes in the relative position of the rostrum with respect to the braincase (rostral flexion). Previous studies have suggested that rostral flexion evolved early in the history of bats in tandem with divergent echolocation modes. We directly quantified rostral flexion and integrated biomechanical modelling, morphometric, and comparative phylogenetic approaches to explore its functional and evolutionary consequences. We found that strong selection associated with echolocation mode explains the early evolution of rostral flexion in bats, with subsequent diversification at different rates within different echolocation emission types. We find extreme rostral flexion is associated with trade-offs in bite performance and overall evolutionary lability of cranial shape. The divergent evolution of rostral flexion across major bat lineages has thus been a major factor structuring the potential evolutionary pathways for the bat cranium. We further suggest that the early evolution of rostral flexion in bats biased the transitions to and from certain echolocation emission modes, and may have differentially affected the degree of dietary ecological diversification among bat clades.
Scalable randomized kernel methods for multiview data integration and prediction with application to Coronavirus disease
Authors: Safo Sandra E , Lu Han
Published: January 2025

There is still more to learn about the pathobiology of coronavirus disease (COVID-19) despite 4 years of the pandemic. A multiomics approach offers a comprehensive view of the disease and has the potential to yield deeper insight into the pathogenesis of the disease. Previous multiomics integrative analysis and prediction studies for COVID-19 severity and status have assumed simple relationships (ie linear relationships) between omics data and between omics and COVID-19 outcomes. However, these linear methods do not account for the inherent underlying nonlinear structure associated with these different types of data. The motivation behind this work is to model nonlinear relationships in multiomics and COVID-19 outcomes, and to determine key multidimensional molecules associated with the disease. Toward this goal, we develop scalable randomized kernel methods for jointly associating data from multiple sources or views and simultaneously predicting an outcome or classifying a unit into one of 2 or more classes. We also determine variables or groups of variables that best contribute to the relationships among the views. We use the idea that random Fourier bases can approximate shift-invariant kernel functions to construct nonlinear mappings of each view and we use these mappings and the outcome variable to learn view-independent low-dimensional representations. We demonstrate the effectiveness of the proposed methods through extensive simulations. When the proposed methods were applied to gene expression, metabolomics, proteomics, and lipidomics data pertaining to COVID-19, we identified several molecular signatures for COVID-19 status and severity. Our results agree with previous findings and suggest potential avenues for future research. Our algorithms are implemented in Pytorch and interfaced in R and available at: https://github.com/lasandrall/RandMVLearn.
Phylogeny of Southeast Asian Mapania (Cyperaceae: Mapanioideae) using chloroplast sequence data
Authors: Shabdin Zinnirah , Márquez-Corro José Ignacio , Larridon Isabel , Simpson David A , Culham Alastair
Published: January 2025

Mapania (Cyperaceae) is a pantropical genus associated with the forest understorey. Its evolutionary history and species delimitation are poorly known in Southeast Asia. To address this lack of knowledge, DNA sequence data from four chloroplast regions (trnL-F, atpH-F, psbA-trnH, and trnK-matK) were generated for a number of populations of 15 species of Mapania. Bayesian and maximum likelihood analyses of the concatenated regions showed a better-resolved phylogeny than previous analyses based on morphological data alone. Mapania bancana was resolved as the sister to the other species of Mapania included in the study. Moreover, this study highlights the need for further investigation of the species limits in this genus. For instance, Mapania cuspidata is retrieved as polyphyletic, and a tentative new species has been detected closely related to Mapania debilis. This study also infers the cradle of the Southeast Asian Mapanias in Borneo, which also holds the largest diversity of the genus in the region. Mapania is still a poorly understood genus that requires further local taxonomic work and more comprehensive fieldwork records to better assess and protect these species.
Multi-omics data integration identifies novel biomarkers and patient subgroups in inflammatory bowel disease
Authors: Preto António José , Chanana Shaurya , Ence Daniel , Healy Matthew D , Domingo-Fernández Daniel , West Kiana A
Published: January 2025

Background

Inflammatory Bowel Disease (IBD), comprising Crohn’s Disease (CD) and Ulcerative Colitis (UC), is a complex condition with diverse manifestations; recent advances in multi-omics technologies are helping researchers unravel its molecular characteristics to develop targeted treatments.

Objective

In this work, we explored one of the largest multi-omics cohorts in Inflammatory Bowel Disease, the Study of a Prospective Adult Research Cohort (SPARC IBD), with the goal of identifying predictive biomarkers for CD and UC and elucidating patient subtypes.

Design

We analyzed genomics, transcriptomics (gut biopsy samples), and proteomics (blood plasma) from hundreds of patients from SPARC IBD. We trained a machine learning model that classifies UC vs. CD samples. In parallel, we integrated multi-omics data to unveil patient subgroups in each of the two indications independently and analyzed the molecular phenotypes of these patient subpopulations.

Results

The high performance of the model showed that multi-omics signatures are able to discriminate between the two indications. The most predictive features of the model, both known and novel omics signatures for IBD, can potentially be used as diagnostic biomarkers. Patient subgroup analysis in each indication uncovered omics features associated with disease severity in UC patients, and with tissue inflammation in CD patients. This culminates with the observation of two CD subpopulations characterized by distinct inflammation profiles.

Conclusion

Our work unveiled potential biomarkers to discriminate between CD and UC and to stratify each population into well-defined subgroups, offering promising avenues for the application of precision medicine strategies.
Cold tolerance and prediction of northern distribution of Histia rhodope (Lepidoptera: Zygaenidae) in China
Authors: Yang Haibo , Chen Zehua , Zhu Pinhong , Guo Shanshan , Wang Yue , Li Dingxu , Ji Siyu , Zhang Guo
Published: January 2025

Histia rhodope (Cramer) (Lepidoptera: Zygaenidae) is one of the most destructive defoliating pests of the landscape tree Bischofia polycarpa (Levl.) S in China and other Southeast Asian regions, posing a critical threat to urban landscapes and their ecological benefits. This pest has shown a trend of northward range shift in recent years in China, making it urgent to understand its potential distribution. This study investigated the cold tolerance of overwintering H. rhodope larvae from October 2022 to March 2023 and estimated their overwintering potential in China. The results showed that the supercooling points (SCP) differed significantly across months. The SCP tended to decrease as the ambient temperature dropped until January, after which it gradually increased until the end of winter. The highest monthly mean SCP was −7.5 ± 2.22°C (October 2022), while the lowest monthly mean SCP was −15.09 ± 2.61°C (January 2023). The mortality rate increased with longer exposure times and lower exposure temperatures but decreased as winter progressed. Moreover, 50% and 90% lethal temperature (Ltemp50 and Ltemp90) exhibited a similar trend, decreasing to a minimum in January 2023, which indicates increased cold tolerance during the colder months. Using Ltemp90 in January as the isotherm for its northern limit indicated that H. rhodope may be limited by low temperatures along the 40°N latitude. These results provide a basis for predicting the dispersal potential and possible geographic range of this pest in China.
Airborne fine particulate matter exposure induces transcriptomic alterations resembling asthmatic signatures: insights from integrated omics analysis
Authors: González Daniel , Infante Alexis , López Liliana , Ceschin Danilo , Fernández-Sanchez María José , Cañas Alejandra , Zafra-Mejía Carlos , Rojas Adriana
Published: January 2025

Fine particulate matter (PM2.5), an atmospheric pollutant that settles deep in the respiratory tract, is highly harmful to human health. Despite its well-known impact on lung function and its ability to exacerbate asthma, the molecular basis of this effect is not fully understood. This integrated transcriptomic and epigenomic data analysis from publicly available datasets aimed to determine the impact of PM2.5 exposure and its association with asthma in human airway epithelial cells. Differential gene expression and binding analyses identified 349 common differentially expressed genes and genes associated with differentially enriched H3K27ac regions in both conditions. Co-expression network analysis revealed three preserved modules (Protein Folding, Cell Migration, and Hypoxia Response) significantly correlated with PM2.5 exposure and preserved in asthma networks. Pathways dysregulated in both conditions included epithelial function, hypoxia response, interleukin-17 and TNF signaling, and immune/inflammatory processes. Hub genes like TGFB2, EFNA5, and PFKFB3 were implicated in airway remodeling, cell migration, and hypoxia-induced glycolysis. These findings elucidate common altered expression patterns and processes between PM2.5 exposure and asthma, helping to understand their molecular connection. This provides guidance for future research to utilize them as potential biomarkers or therapeutic targets and generates evidence supporting the need for implementing effective air quality management strategies.
Associations between cardiac rehabilitation structure and processes and dietary habits after myocardial infarction: a nationwide registry study
Authors: Hag Emma , Bäck Maria , Henriksson Peter , Wallert John , Held Claes , Stomby Andreas , Leosdottir Margret
Published: January 2025

Aims

Improved dietary habits are important for successful secondary prevention after myocardial infarction (MI), with counselling and support on healthy dietary habits constituting a cornerstone of cardiac rehabilitation (CR). However, there is limited knowledge on how to optimize CR organization to motivate patients to adopt healthy dietary habits. We aimed to explore associations between CR programme structure, processes, and self-reported dietary habits 1 year post-MI.

Methods and results

Organizational data from 73 Swedish CR centres and patient-level data from 5248 CR patients were analysed using orthogonal partial least squares discriminant analysis to identify predictors for healthy dietary habits. Variables of importance for the projection (VIP) values exceeding 0.80 were considered meaningful. Key predictors included the CR centre having a medical director [VIP (95% confidence interval)] [1.86 (1.1–2.62)], high self-reported team spirit [1.63 (1.29–1.97)], nurses have formal training in counselling methods [1.20 (0.75–1.65)], providing discharge information on risk factors [2.23 (1.82–2.64)] and lifestyle [1.81 (1.31–2.31)], time dedicated to patient interaction during follow-up [1.60 (0.80–2.40)], and centres aiming for patients to have the same nurse throughout follow-up [1.54 (1.17–1.91)]. The more positive predictors a CR centre reported to follow, the further improvement in patient-level dietary habits, were analysed by multivariable regression analysis [odds ratio for each additional positive predictor reported 1.03 (1.02–1.05), P < 0.001].

Conclusion

Several variables related to CR structure and processes were identified as predictors for patients reporting healthier dietary habits. These findings offer guidance for CR centres in resource allocation and optimizing patient benefits of CR attendance.
Estimating financial and health burden by initial Medicare plan choice and history of cancer
Authors: Jazowski Shelley A , Achola Emma M , Nicholas Lauren Hersch , Wood William A , Friese Christopher R , Dusetzina Stacie B
Published: January 2025

Understanding the downstream consequences of initial Medicare plan selection is necessary to ensure access to and affordability of health care services, especially for older adults with serious illness. We used 2008-2020 data from the Health and Retirement Study to estimate financial and health burden by initial Medicare plan selection (traditional Medicare without supplemental coverage, traditional Medicare plus supplemental coverage, or Medicare Advantage) and self-reported history of cancer. Initially choosing benefits with greater financial protections (either traditional Medicare plus supplemental coverage or Medicare Advantage) relative to traditional Medicare without supplemental coverage was associated with lower levels of out-of-pocket spending and a lower likelihood of reporting cost-related medication nonadherence and fair or poor health. Policymakers should consider improving the adequacy of traditional Medicare coverage to ensure the affordability of health care services and reduce the burden of serious illness among older adults, especially those with a history of cancer.
Long-term care plan recommendation for older adults with disabilities: a bipartite graph transformer and self-supervised approach
Authors: Miao Chunlong , Luo Jingjing , Liang Yan , Liang Hong , Cen Yuhui , Guo Shijie , Yu Hongliu
Published: January 2025

Background

With the global population aging and advancements in the medical system, long-term care in healthcare institutions and home settings has become essential for older adults with disabilities. However, the diverse and scattered care requirements of these individuals make developing effective long-term care plans heavily reliant on professional nursing staff, and even experienced caregivers may make mistakes or face confusion during the care plan development process. Consequently, there is a rigid demand for intelligent systems that can recommend comprehensive long-term care plans for older adults with disabilities who have stable clinical conditions.

Objective

This study aims to utilize deep learning methods to recommend comprehensive care plans for the older adults with disabilities.

Methods

We model the care data of older adults with disabilities using a bipartite graph. Additionally, we employ a prediction-based graph self-supervised learning (SSL) method to mine deep representations of graph nodes. Furthermore, we propose a novel graph Transformer architecture that incorporates eigenvector centrality to augment node features and uses graph structural information as references for the self-attention mechanism. Ultimately, we present the Bipartite Graph Transformer (BiT) model to provide personalized long-term care plan recommendation.

Results

We constructed a bipartite graph comprising of 1917 nodes and 195 240 edges derived from real-world care data. The proposed model demonstrates outstanding performance, achieving an overall F1 score of 0.905 for care plan recommendations. Each care service item reached an average F1 score of 0.897, indicating that the BiT model is capable of accurately selecting services and effectively balancing the trade-off between incorrect and missed selections.

Discussion

The BiT model proposed in this paper demonstrates strong potential for improving long-term care plan recommendations by leveraging bipartite graph modeling and graph SSL. This approach addresses the challenges of manual care planning, such as inefficiency, bias, and errors, by offering personalized and data-driven recommendations. While the model excels in common care items, its performance on rare or complex services could be enhanced with further refinement. These findings highlight the model's ability to provide scalable, AI-driven solutions to optimize care planning, though future research should explore its applicability across diverse healthcare settings and service types.

Conclusions

Compared to previous research, the novel model proposed in this article effectively learns latent topology in bipartite graphs and achieves superior recommendation performance. Our study demonstrates the applicability of SSL and graph transformers in recommending long-term care plans for older adults with disabilities.
Commentary on ‘Structural insights into a bacterial β-glucosidase capable of degrading sesaminol triglucoside to produce sesaminol: towards the understanding of the aglycone recognition mechanism by the C-terminal lid domain’
Authors: Nagae Masamichi
Published: January 2025

Sesaminol is an organic compound that shows the strong antioxidant, anti-inflammatory and neuroprotective properties. Sesaminol triglucoside (STG) is a glycosylated form of sesaminol and abundantly exists in sesame seeds. However, typical β-glucosidases could not deglycosylate STG probably due to its bulky aglycone. PSTG1 and 2 are β-glucosidases lately isolated from Paenibacillis sp. KB0459 and have the capacity to deglycosylate STG. A recent report by Yanai et al. (J. Biochem. 2023; 174:335–344) revealed the unique domain architecture of PSTG1. Apart from other β-glucosdasies in the GH3 family, PSTG1 has a novel accessary domain (domain 4) at the C-terminus. Domain 4 contributes to the dimer formation and is located close to the active site. Interestingly, several hydrophobic residues are exposed, suggesting that this domain may recognize the hydrophobic aglycone of STG. The physiological functions of the non-catalytic domains in glyco-enzymes are sometimes overlooked. This paper sheds light on the aglycone recognition by novel accessary domain.
In the Company of Strangers: Social Influence from Anonymous Peers in Online Game Settings
Authors: Jo Wooyong , Sunder Sarang , Choi Jeonghye , Trivedi Minakshi
Published: January 2025

Social interactions among consumers, especially in the consumption of digital goods, have become commonplace in an increasingly interconnected marketplace. As such, understanding the impact of such interactions on consumer behavior carries major academic and practitioner significance. This research focuses on an important but under-researched aspect of social influence and the underlying mechanisms that may be driving peer effects. Using the context of a massive online peer-to-peer game, we estimate peer effects arising from anonymous peers. The findings suggest a robust and significant influence of anonymous peers on one’s own purchase behavior. Further, we find that peer effects arising from anonymous peers are largely driven by informational reasons as opposed to competitive concern even in a competitive online gaming context. That is, players rely on others’ purchase decisions despite anonymity; moreover, such influence is more pronounced for inexperienced players with little contextual knowledge. To demonstrate the effectiveness of leveraging the nature of peer influence in online game settings, we provide an illustrative example using an intervention simulation. Finally, we discuss the implications of our findings for marketing academia and practitioners in the video game industry.
Predatory capacity of Lasioseius lindquisti (Acari: Blattisociidae) and Lasioseius scapulatus (Acari: Blattisociidae) on Megalurothrips usitatus (Thysanoptera: Thripidae)
Authors: Zhu Yilin , Chi Yuanming , Yu Chen , Feng Mingyue , Li Maoqing , Chen Yanyu , Shi Wangpeng
Published: January 2025

Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae) is an important pest of cowpeas, Vigna unguiculata (L.) Walp., and can cause severe damage to the crop. Lasioseius lindquisti (Tseng) (Acari: Blattisociidae) and Lasioseius scapulatus (Kennett) (Acari: Blattisociidae) are 2 mites used against M. usitatus in Hainnan, China. The functional responses of these mites were examined in the laboratory. Lasioseius lindquisti showed a type III functional response, with a maximum prey consumption of 22.38 ± 0.63 per day. Its optimal search density for each unit in this experiment was 10.27 ± 0.50 per day. Lasioseius scapulatus showed a type II functional and an attack rate on 1st instars of M. usitatus of 0.83 ± 0.23. The handling time (h) of L. scapulatus was 0.074 ± 0.018 (means ± SE), while the maximum attack rate (T/Th) of adult females on 1st instar thrips was 13.51. Our results showed that both L. lindquisti and L. scapulatus are potentially useful predators of M. usitatus.
Research on the multiscale mechanical properties of paleosols based on the freeze‒thaw cycle
Authors: Guo Zhuang , Song Jia , Bai Yang , Zhou Zihao
Published: January 2025

To study the failure mechanism of paleosol landslides, taking the paleosol of a landslide body in Yan'an as an example, scanning electron microscopy (SEM), nuclear magnetic resonance (NMR), and conventional triaxial tests were used to obtain particle composition, microstructure scanning results, T2 spectral distribution, and stress-strain curves under different freeze-thaw cycles. The results showed that with the increase of freeze-thaw cycles, the number of micropores in paleosol increased to 70.5% and stabilized, while the number of micropores decreased to 18.4%, mesopores decreased to 7.5%, macropores decreased to 3.6%, and eventually stabilized. The fractal dimension of pore shape distribution in paleosol increases along a convex curve to 1.42. The T2 spectrum presents three stepped small peaks, with the peak spectral area of relaxation time ranging from 0.01 ms to 3.16 ms being the largest, indicating that small pores dominate. As the number of freeze-thaw cycles increases, the peak area of smaller relaxation times expands, indicating that freeze-thaw cycles have destroyed the structure of paleosols and generated a large number of tiny pores. Under conditions of higher confining pressure and lower moisture content, when there are fewer freeze-thaw cycles, the strain corresponds to higher stress. The freeze-thaw cycle makes the stress-strain curve of paleosol harder, indicating that the original structure is damaged and the new structure appears as disordered particles.
The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the L-amino acid transporters
Authors: Fort Joana , Nicolàs-Aragó Adrià , Maggi Luca , Martinez-Molledo Maria , Kapiki Despoina , González-Novoa Paula , Gómez-Gejo Patricia , Zijlstra Niels , Bodoy Susanna , Pardon Els , Steyaert Jan , Llorca Oscar , Orozco Modesto , Cordes Thorben , Palacín Manuel
Published: January 2025

L-Amino acid transporters (LATs) play a key role in a wide range of physiological processes. Defects in LATs can lead to neurological disorders and aminoacidurias, while the overexpression of these transporters is related to cancer. BasC is a bacterial LAT transporter with an APC fold. In this study, to monitor the cytoplasmic motion of BasC, we developed a single-molecule Förster resonance energy transfer assay that can characterize the conformational states of the intracellular gate in solution at room temperature. Based on combined biochemical and biophysical data and molecular dynamics simulations, we propose a model in which the conserved lysine residue in TM5 supports TM1a to explore both open and closed states within the cytoplasmic gate under apo conditions. This equilibrium can be altered by substrates, mutation of conserved lysine 154 in TM5, or a transport-blocking nanobody interacting with TM1a. Overall, these findings provide insights into the transport mechanism of BasC and highlight the significance of the lysine residue in TM5 in the cytoplasmic gating of LATs.
Surfacic networks
Authors: Barthelemy Marc , Boeing Geoff , Chiaradia Alain , Webster Christopher J
Published: January 2025

Surfacic networks are structures built upon a 2D manifold. Many systems, including transportation networks and various urban networks, fall into this category. The fluctuations of node elevations imply significant deviations from typical plane networks and require specific tools to understand their impact. Here, we present such tools, including lazy paths that minimize elevation differences, graph arduousness which measures the tiring nature of shortest paths (SPs), and the excess effort, which characterizes positive elevation variations along SPs. We illustrate these measures using toy models of surfacic networks and empirically examine pedestrian networks in selected cities. Specifically, we examine how changes in elevation affect the spatial distribution of betweenness centrality. We also demonstrate that the excess effort follows a nontrivial power law distribution, with an exponent that is not universal, which illustrates that there is a significant probability of encountering steep slopes along SPs, regardless of the elevation difference between the starting point and the destination. These findings highlight the significance of elevation fluctuations in shaping network characteristics. Surfacic networks offer a promising framework for comprehensively analyzing and modeling complex systems that are situated on or constrained to a surface environment.
Child Rights in Practice: Navigating Beyond Definitions of Child Labour in Bangladesh’s Legal Landscape
Authors: Alam Md. Tasnvir
Published: January 2025

This study explores the intricate legal landscape that governs child labour in Bangladesh, tracing its historical roots to British colonial rule and highlighting the prevalence of conflicting definitions and provisions within the current legal system. Through qualitative research methods, including key informant interviews and in-depth interviews, this study delves into the multifaceted dimensions of child labour regulation in Bangladesh. The findings reveal discrepancies in understanding among stakeholders, and family members often citing poverty and illiteracy as barriers to understanding legal provisions. In contrast, employers demonstrate varying degrees of awareness, particularly following encounters with law enforcement agencies. Legal experts advocate for a universal definition of childhood in statutory law to address this complexity effectively. Furthermore, the study uncovers widespread ignorance and misinformation about the age verification process for child labourers, along with prevalent instances of document forgery and lenient age verification processes. Most importantly, the dynamics of the penalty system for child labour violations also reveal divergent perspectives among stakeholders, highlighting the need for comprehensive reforms in statutory law, including amendments to definitions, implementation of stringent age verification processes, and increased penalty thresholds.
Raman Spectroscopies for Cancer Research and Clinical Applications: a Focus on Cancer Stem Cells
Authors: Pagliari Francesca , Tirinato Luca , Di Fabrizio Enzo
Published: January 2025

Over the last two decades, research has increasingly focused on Cancer Stem Cells (CSCs), considered responsible for tumor formation, resistance to therapies, and relapse. The traditional "static" CSC model used to describe tumor heterogeneity has been challenged by the evidence of CSC dynamic nature and plasticity. A comprehensive understanding of the mechanisms underlying this plasticity, and the capacity to unambiguously identify cancer markers to precisely target CSCs are crucial aspects for advancing cancer research and introducing more effective treatment strategies. In this context, Raman spectroscopy (RS) and specific Raman schemes, including CARS, SRS, SERS, have emerged as innovative tools for molecular analyses both in vitro and in vivo. In fact, these techniques have demonstrated considerable potential in the field of cancer detection, as well as in intraoperative settings, thanks to their label-free nature and minimal invasiveness. However, the RS integration in pre-clinical and clinical applications, particularly in the CSC field, remains limited.

This review provides a concise overview of the historical development of RS and its advantages. Then, after introducing the CSC features and the challenges in targeting them with traditional methods, we review and discuss the current literature about the application of RS for revealing and characterizing CSCs and their inherent plasticity, including a brief paragraph about the integration of artificial intelligence with RS.

By providing the possibility to better characterize the cellular diversity in their microenvironment, RS could revolutionize current diagnostic and therapeutic approaches, enabling early identification of CSCs and facilitating the development of personalized treatment strategies.
Biosensor characterization: formal methods from the perspective of proteome fractions
Authors: Vaccari Nicolás A , Zevallos-Aliaga Dahlin , Peeters Tom , Guerra Daniel G
Published: January 2025

Many studies characterize transcription factors and other regulatory elements to control gene expression in recombinant systems. However, most lack a formal approach to analyse the inherent and context-specific variations of these regulatory components. This study addresses this gap by establishing a formal framework from which convenient methods are inferred to characterize regulatory circuits. We modelled the bacterial cell as a collection of proteome fractions. Deriving the time-dependent proteome fraction, we obtained a general theorem that describes its change as a function of its expression fraction, a specific portion of the total biosynthesis flux of the cell. Formal deduction reveals that when the proteome fraction reaches a maximum, it becomes equivalent to its expression fraction. This equation enables the reliable measurement of the expression fraction through direct protein quantification. In addition, the experimental data demonstrate a linear correlation between protein production rate and specific growth rate over a significant time period. This suggests a constant expression fraction within this window. For an Isopropyl β- d-1-thiogalactopyranoside (IPTG) biosensor, in five cellular contexts, expression fractions determined by the maximum method and the slope method produced strikingly similar dose–response parameters when independently fit to a Hill function. Furthermore, by analysing two more biosensors, for mercury and cumate detection, we demonstrate that the slope method can be applied effectively to various systems. Therefore, the concepts presented here provide convenient methods for obtaining dose–response parameters, clearly defining the time interval of their validity and offering a framework for interpreting typical biosensor outputs in terms of bacterial physiology.

Graphical Abstract Nutrients, transformed by the action of the Nutrient Fixators (purple arrow), are used at a rate of ρ for Protein biosynthesis. The total rate ρ is multiplied by expression fractions fR, fC, fH, and fQ to obtain the biosynthesis rate (black arrows) of each proteome fraction ΦR, ΦC, ΦH, ΦQ, respectively. In a graph of Growth rate versus Proteome Fraction Production Rate, a linear function (green lines) can be observed, and its slope is equal to the expression fraction at each condition.
The impact of state income tax breaks on savings and income security in retirement
Authors: Dao Ngoc , Collins J Michael
Published: January 2025

State policies exempting retirement income from taxation have the potential to change how people save and spend down their savings in retirement. Using Social Security earnings records linked to the Health and Retirement Survey, this study shows people in states with income tax exemptions on retirement income increase in contributions to tax-deferred retirement accounts. While people in these states accumulate more savings in expectation of being able to increase income in retirement without incurring higher state income taxes, they do not have more income in retirement, either pre- or post-income taxes. Seniors in exemption states relative to seniors in other states do not have lower rates of hardship or show higher standards of living, although they tend to retire slightly earlier. These findings suggest that exempting retirement income from taxation may not improve people’s economic well-being in their retirement years.
Identification and Molecular Marker Detection of Leaf Rust Resistance Genes in Wheat Lines from China: Development of an Efficient Software for Gene Postulation
Authors: Gao Pu , Liu Peng-peng , Dong Rui , Gebrewahid Takele Weldu , Wang Xin-hai , Wang Xue-qing , Zhang Jia-yao , Zhang Pei-pei , Sang Wei , Li Zai-feng
Published: January 2025

Wheat leaf rust, caused by Puccinia triticina Erikss. (Pt), is one of the most devastating diseases in common wheat (Triticum aestivum L.) globally. Using resistant lines is the most cost-effective and safe disease control method. Eighty-three wheat lines from China and 36 differential lines, mainly near-isogenic lines (NILs) with known leaf rust resistance (Lr) genes in the Thatcher background, were inoculated with 17 Pt races at the seedling stage to postulate Lr gene(s) in the greenhouse. Field tests conducted during the 2020-2021 and 2021-2022 cropping seasons assessed adult-plant resistance to leaf rust. Moreover, we developed a graphical user interface (GUI) bioinformatics toolkit platform called WEKits v1.0, which integrates a gene postulation submodule based on the gene-for-gene hypothesis, providing accurate and efficient analysis. Through gene postulation, molecular marker detection, and pedigree analysis, we identified the presence of nine Lr genes Lr1, Lr10, Lr14a, Lr21, Lr26, Lr34, Lr37, Lr44, and Lr13/LrZH22, either individually or in combination in 30 wheat lines. Furthermore, 19 lines exhibited slow rusting resistance in both growing seasons. The development of the WEKits software significantly enhanced the efficiency and accuracy of the gene postulation process, providing a valuable tool for rapid identification of known resistance genes in the wheat lines. This could create a vital input to wheat rust resistance breeding. The results identified in this study and the WEKits platform are valuable for selecting lines with effective Lr genes and breeding rust-resistant wheat.
Influence of Sweetpotato Resistance on the Development of Meloidogyne enterolobii and M. incognita
Authors: Galo David , Santos Rezende Josie , Watson Tristan T.
Published: January 2025

Meloidogyne enterolobii and M. incognita are major pests of sweetpotato. The ability of M. enterolobii to cause symptoms and reproduce on nematode-resistant cultivars threatens the sweetpotato industry. To evaluate the penetration, development, and reproduction of M. enterolobii and M. incognita on sweetpotato, a time-course study was conducted using the genotypes ‘LA14-31’ (resistant to M. enterolobii and intermediate-resistant to M. incognita), ‘LA18-100’ (susceptible to M. enterolobii and resistant to M. incognita), and ‘LA19-65’ (resistant to M. enterolobii and susceptible to M. incognita), with ‘Beauregard’ (susceptible to both species) and ‘Jewel’ (resistant to M. enterolobii and intermediate-resistant to M. incognita) as controls. Sweetpotato roots were collected at 7-, 9-, 11-, 13-, 21-, and 35-days post-inoculation (DPI), stained with acid fuchsin, and analyzed for nematode developmental stages. Nematode reproduction was evaluated by examining egg production at 42 DPI. Results showed that M. enterolobii developed and reproduced only in ‘Beauregard’ and ‘LA18-100’. In resistant genotypes such as ‘Jewel’, ‘LA14-31’, and ‘LA19-65’, M. enterolobii remained at the pre-parasitic J2-stage, with halted development linked to localized cell death in response to M. enterolobii penetration. For M. incognita, the defense response was most notable in ‘LA18-100’, where infective juveniles either died, matured as males, or experienced delayed development into adult females, with a marked reduction in M. incognita reproduction. These findings suggest that resistance to M. enterolobii likely involves a hypersensitive-like response that prevents feeding site establishment, whereas resistance to M. incognita appears quantitative, as evidenced by delayed nematode development and reduced reproduction in resistant genotypes.
Preterm Birth Frequency and Associated Outcomes From the MATISSE (Maternal Immunization Study for Safety and Efficacy) Maternal Trial of the Bivalent Respiratory Syncytial Virus Prefusion F Protein Vaccine
Authors: Madhi Shabir A. , Kampmann Beate , Simões Eric A.F. , Zachariah Philip , Pahud Barbara A. , Radley David , Sarwar Uzma N. , Shittu Emma , Llapur Conrado , Pérez Marc Gonzalo , Maldonado Yvonne , Kachikis Alisa , Zar Heather J. , Swanson Kena A. , Lino Maria Maddalena , Anderson Annaliesa S. , Gurtman Alejandra , Munjal Iona
Published: January 2025

OBJECTIVE:

To describe preterm birth frequency and newborn and infant outcomes overall and among preterm children in the MATISSE (Maternal Immunization Study for Safety and Efficacy) trial of maternal vaccination with bivalent respiratory syncytial virus (RSV) prefusion F protein–based vaccine (RSVpreF) to protect infants against severe RSV-associated illness.

METHODS:

MATISSE was a global, phase 3, randomized, double-blind trial. Pregnant individuals received single injections of RSVpreF or placebo. Adverse events of special interest, including preterm birth (gestational age less than 37 weeks) and low birth weight (2,500 g or less), were collected through 6 months after delivery (pregnant participants) and from birth through age 12 or 24 months (pediatric participants).

RESULTS:

Overall, 7,386 pregnant participants received RSVpreF (n=3,698) or placebo (n=3,688); 7,305 newborns and infants were included in the analysis. Most children in both groups were born full term (more than 93%) with normal birth weight (95% or higher). Newborn and infant outcomes, including rates of low birth weight and neonatal hospitalization, were favorable and comparable between groups. Preterm birth rates were 5.7% in the RSVpreF arm and 4.7% in the placebo arm (relative risk [RR] 1.20, 95% CI, 0.98–1.46); most were late preterm. Newborn and infant outcomes, including rates of low birth weight and neonatal hospitalization, were comparable between groups. Twenty-two newborn or infant deaths occurred during the study (RSVpreF n=8, placebo n=14). When stratified by income region, preterm birth rates in RSVpreF and placebo recipients were both 5.0% in high-income countries. Rates in non–high-income countries were 7.0% and 4.0% in the RSVpreF and placebo groups, respectively, and 8.3% and 4.0% in South Africa (RR 2.06, 95% CI, 1.21–3.51).

CONCLUSION:

In this study of maternal RSVpreF vaccination, no clinically significant increase in adverse events of special interest, including preterm birth, low birth weight, or neonatal hospitalization, was observed among pregnant people in the overall analysis. In subgroup analysis of non–high-income countries, an elevated risk of preterm birth was observed. More research is needed to better ascertain preterm delivery risk factors, particularly aimed at minimizing disparities among geographic regions.

FUNDING SOURCE:

This study was sponsored by Pfizer.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT04424316.