Category: Statistics

Sci Rep. 2025 Feb 17;15(1):5810. doi: 10.1038/s41598-025-89678-7.

ABSTRACT

The illegal ivory trade has led to a sharp decline in wild elephant populations in recent decades, while mammoth (Mammuthus primigenius) ivory products have increasingly flooded the marketplace, complicating identification efforts by frontline law enforcement. Existing ivory identification methods face several challenges, including inconsistent accuracy due to sample quality, high costs, slow turnaround times, and destructive sample requirements. Currently, there is a lack of a fast, convenient, and highly effective solution to address these issues. To tackle these challenges, this study developed a novel, efficient, and accurate method for identifying and characterizing ivory products using ultra-performance liquid chromatography with a fluorescence detector (UPLC-FLR). The technique focuses on various organic small-molecule compounds in ivory that have been largely overlooked. A chemical fingerprint library was created using 72 African elephant and 69 mammoth ivory samples. Comprehensive comparative analyses, including principal component analysis, compound distribution analysis, proportion analysis, chord diagrams, and statistical significance tests, revealed significant differences between the organic compounds in the two sample groups, confirming the method’s reliability. Six widely used machine learning classification models were then applied to construct a discriminant model based on 11 key feature compounds among the 85 identified, with each model achieving 100% classification accuracy. Compared to the conventional ‘gold standard’ molecular biology method, this UPLC-based approach shortened detection time from 24 h to just 1 h, reduced the sample requirement by 50%, and cut costs by 90%, making it a more efficient, user-friendly solution for frontline law enforcement. Widespread adoption of this method in law enforcement could become a powerful tool in the fight against the illegal ivory trade.

PMID:39962129 | DOI:10.1038/s41598-025-89678-7

Sci Rep. 2025 Feb 17;15(1):5790. doi: 10.1038/s41598-025-87154-w.

ABSTRACT

Fluorescence recovery after photobleaching (FRAP) allows to study actin-turnover in dendritic spines by providing recovery trajectories over time within a nested data structure (i.e. spine/neuron/culture). Statistical approaches to FRAP usually consider one-phase association models to estimate recovery-curve-specific parameters and test statistical hypotheses on curve parameters either at the spine or neuron level, ignoring the nested data structure. However, this approach leads to pseudoreplication concerns. We propose a nonlinear mixed-effects model to integrate the one-phase association model estimate with the nested data structure of FRAP experiments; this also allows us to model heteroscedasticity and time dependence in the data. We used this approach to evaluate the effect of the downregulation of the actin-binding protein CAP2 on actin dynamics. Our model allows the additional modelling of the variance function across experimental conditions, which may represent a novel parameter of interest in FRAP experiments. Indeed, the detected differential effect of the experimental condition on the variance component captures the increased instability of time-specific observations around the spine-specific trajectory for the CAP2-downregulated spines compared to the control spines. We hypothesise that this parameter reflects the increased instability of the actin cytoskeleton in dendritic spines upon CAP2 downregulation. We developed an R-based Shiny application, termed FRApp, to fit the statistical models introduced without requiring programming expertise.

PMID:39962126 | DOI:10.1038/s41598-025-87154-w

Transl Psychiatry. 2025 Feb 17;15(1):55. doi: 10.1038/s41398-025-03259-w.

ABSTRACT

Narcolepsy is a severe sleep disorder with characteristics of fatigue, fragmented sleep, cataplexy and hypnagogic hallucinations. Earlier clinical studies have reported the onset of schizophrenia after narcolepsy but the causality behind narcolepsy and schizophrenia is unknown. Our goal was to understand the causality between narcolepsy and schizophrenia. To estimate the comorbidity between narcolepsy and schizophrenia, we employed data from the FinRegistry that contains data for the total population of Finland in total 7.2 million individuals (N = 1664 individuals with narcolepsy and 55,372 with schizophrenia). We then used Mendelian randomization and previously published genome-wide association data to test the causality between narcolepsy and schizophrenia. We observed a robust causal association from narcolepsy to schizophrenia using the HLA-independent lead variants (P-value = 6.0 × 10^-4), which was accentuated when including the HLA locus (P-value = 4.48 × 10^-7). Furthermore, we observed a modest bidirectional causality from schizophrenia to narcolepsy (P-value = 0.015). There was no evidence of pleiotropy. Our findings indicate a causal relationship where narcolepsy may increase the risk for schizophrenia, and a bidirectional causality from schizophrenia to narcolepsy. Additionally, our results clarify the psychiatric burden in narcolepsy.

PMID:39962082 | DOI:10.1038/s41398-025-03259-w

Nat Commun. 2025 Feb 17;16(1):1711. doi: 10.1038/s41467-025-56986-5.

ABSTRACT

Epistasis – the interaction between alleles at different genetic loci – plays a fundamental role in biology. However, several recent approaches quantify epistasis using a chimeric formula that measures deviations from a multiplicative fitness model on an additive scale, thus mixing two scales. Here, we show that for pairwise interactions, the chimeric formula yields a different magnitude but the same sign of epistasis compared to the multiplicative formula that measures both fitness and deviations on a multiplicative scale. However, for higher-order interactions, we show that the chimeric formula can have both different magnitude and sign compared to the multiplicative formula. We resolve these inconsistencies by deriving mathematical relationships between the different epistasis formulae and different parametrizations of the multivariate Bernoulli distribution. We argue that the chimeric formula does not appropriately model interactions between the Bernoulli random variables. In simulations, we show that the chimeric formula is less accurate than the classical multiplicative/additive epistasis formulae and may falsely detect higher-order epistasis. Analyzing multi-gene knockouts in yeast, multi-way drug interactions in E. coli, and deep mutational scanning of several proteins, we find that approximately 10% to 60% of inferred higher-order interactions change sign using the multiplicative/additive formula compared to the chimeric formula.

PMID:39962081 | DOI:10.1038/s41467-025-56986-5

Soc Sci Med. 2025 Feb 8;369:117826. doi: 10.1016/j.socscimed.2025.117826. Online ahead of print.

ABSTRACT

BACKGROUND AND PURPOSE: Engagement in internal quality improvement (QI) within physician practices is a key avenue by which to deliver evidence-based and patient-centered care, but it can be difficult to sustain such engagement. Consequently, research is needed that identifies organizational factors associated with sustained internal QI. We utilized two waves of a national survey of physician practices to explore whether organizational innovation characteristics including organizational culture, health information technology (HIT) capacity, and Accountable Care Organization (ACO) affiliation distinguish physician practices that sustain their engagement in internal QI from those that do not.

METHODS: We linked two waves of the National Survey of Healthcare Organizations and Systems (NSHOS) fielded between 2017-2018 and 2022-2023 among physician practices in the United States to assess organizational characteristics associated with sustained engagement in QI (n = 714 practices). Our final regression models incorporate survey and nonresponse weights and control for practice size and ownership.

RESULTS: We found that higher innovative culture scores were associated with almost three times the odds of sustained QI (OR = 2.91, p < 0.001). Although high HIT capacity was also associated with greater odds of sustained versus non-sustained QI across both survey waves, this finding was not statistically significant (OR = 1.11, p > 0.05). We did not find statistically significant support for our final hypothesis that ACO affiliation (whether commercial, Medicare, or Medicaid) was associated with sustained internal QI (OR = 1.26, p > 0.05).

CONCLUSIONS: Our study is the first to our knowledge to underscore the critical importance of innovative organizational culture to sustaining internal QI among physician practices. Although ACO affiliation may signal willingness to participate in QI as a means to advance evidence- and value-based care and HIT capacity may facilitate improvement activities, these characteristics may not assure sustained internal QI engagement without an organizational culture aligned with QI.

PRACTICE IMPLICATIONS: Policies that advance organizational capacity to develop a learning-oriented innovative culture could enable sustained QI engagement at the physician practice level.

PMID:39961151 | DOI:10.1016/j.socscimed.2025.117826

Arch Oral Biol. 2025 Feb 12;173:106196. doi: 10.1016/j.archoralbio.2025.106196. Online ahead of print.

ABSTRACT

OBJECTIVES: To assess the efficacy of the AuNP-enhanced ELISA in the detection of salivary TNF-α in OSCC and evaluate its predictive value for survival.

DESIGN: A longitudinal study was conducted on 40 OSCC patients and 10 healthy controls. Saliva was collected at a regular interval and TNF alpha levels were measured using ELISA and AuNP-enhanced ELISA. Descriptive statistics were carried out for demographic, clinical, and biomarker data. The efficacy of ELISA and AuNP-enhanced ELISA was estimated and compared using the ROC curve. Kaplan-Meier survival analysis and Cox proportional hazards models were used to assess the survival outcome. A neural network model was performed to estimate TNF-α levels over time in OSCC patients.

RESULTS: OSCC patients (ELISA is 47.52 ± 20.23 and Gold nano-enhanced ELISA is 57.63 ± 24.99) exhibited significantly elevated TNFα levels compared to controls (ELISA is 10.13 ± 3.07and Gold nano-enhanced ELISA is 12.07 ± 3.66). Gold nano-enhanced ELISA (AUC of 0.995) demonstrated superior sensitivity than ELISA (AUC of 0.986), while Gold nano-enhanced ELISA achieves an even higher in detecting elevated TNFα levels. Kaplan-Meier analysis shows that Gold nano-enhanced ELISA outperforms ELISA in capturing survival trends, with better survival for TNF-α levels above the cutoff at 9 months (70 % vs. 60 %) and 24 months (40 % vs. 0 %). The neural network model poorly predicted TNF- levels over the period (AUC = 0.447).

CONCLUSIONS: The gold nano-enhanced TNFα detection method is effective in detecting TNFα levels between OSCC patients and controls, demonstrating superior sensitivity in identifying survival trends over time compared to traditional ELISA.

PMID:39961150 | DOI:10.1016/j.archoralbio.2025.106196

Aust Health Rev. 2025 Feb 18. doi: 10.1071/AH24329. Online ahead of print.

ABSTRACT

ObjectiveBreast cancer is the most common cancer in Australian women, with rising prevalence and costs. Inefficient care leads to poorer outcomes and strains healthcare systems. This review explores the association between breast cancer management strategies and efficiency in delivering care.MethodsAn exploratory single database review following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) guidelines was conducted by searching MEDLINE for studies on patient-centred care, efficiency, and breast cancer published 2014-present. Data extraction and synthesis followed PRISMA extension for Scoping Reviews (PRISMA-ScR) Checklist.ResultsEleven studies were included (one systematic review, one randomised control trial (RCT), four comparative studies, three observational studies, one budget analysis, and one protocol). Seven studies found a positive association between patient-centred care and efficiency; six showed statistical significance. These included reduced diagnostic delays (n=3), improved shared decision-making with decision aids (n=3), need to address ethnic/socioeconomic status disparities (n=2), and survivorship interventions/experience (n=3).ConclusionThis is the first review analysing multiple strategies to improve delivery of care, demonstrating improved efficiency throughout the treatment journey in breast cancer by using patient-centred care. Further implementation studies are needed to understand how to optimise outcomes and healthcare sustainability.

PMID:39961135 | DOI:10.1071/AH24329

Health Informatics J. 2025 Jan-Mar;31(1):14604582241304708. doi: 10.1177/14604582241304708.

ABSTRACT

Introduction: Current discussions surround whether ‘person-first language’ (PFL) such as ‘patient with autism’ and ‘identity-first language’ (IFL) such as ‘autistic patient’ is most sensitive and appropriate. There is language guidance when talking about disability and race, ethnicity, and ancestry in genetics research, but not around PFL and IFL. We applied natural language processing (NLP) methods to PFL and IFL in published in genetics research, focussing on Autism Spectrum Disorders (ASD). Methods: Of the approximately 38,000 abstracts accepted in European Society of Human Genetics (ESHG) conference between 2001 and 2021, almost 5000 contained autism keywords. NLP analysis of these explored PFL and IFL use over time, in combination with specific nouns, and in combination with each other. Results: 262 instances of PFL and 264 instances of IFL showed similar, common and consistent use over time. Straightforward matches (e.g. ‘patient with ASD’ or ‘ASD patient’) accounted for most uses, with subtle differences in the frequently co-occurring nouns. 50 abstracts used both patterns, typically with one example of each. Conclusions: NLP can quantify use, timing and context for PFL and IFL in research articles. Consequently, NLP can support the development of language style guidelines or to evaluate their effectiveness.

PMID:39961131 | DOI:10.1177/14604582241304708

Ann Intern Med. 2025 Feb 18. doi: 10.7326/ANNALS-24-02426. Online ahead of print.

ABSTRACT

BACKGROUND: The Centers for Medicare & Medicaid Services (CMS) Severe Sepsis and Septic Shock Management Bundle (SEP-1) is now included in the Hospital Value-Based Purchasing (VBP) Program.

PURPOSE: To assess the evidence supporting SEP-1 compliance or SEP-1 implementation in improving sepsis mortality.

DATA SOURCES: PubMed, Web of Science, EMBASE, CINAHL Complete, and Cochrane Library from inception to 26 November 2024.

STUDY SELECTION: Studies of adults with sepsis that included 3- or 6-hour sepsis bundles defined by SEP-1 specifications.

DATA EXTRACTION: Article screening, full-text review, data extraction, and risk-of-bias assessment were independently performed by 2 authors. Level of evidence was determined using GRADE (Grading of Recommendations Assessment, Development and Evaluation) criteria and National Quality Forum criteria.

DATA SYNTHESIS: A total of 4403 unique references were screened, and 17 studies were included. Twelve studies assessed the relationship between SEP-1 compliance and mortality; 5 showed statistically significant benefit, whereas 7 did not. Among studies showing benefit, 1 did not adjust for confounders, 1 found benefit only among patients with severe sepsis, 1 included only patients with septic shock, and 1 included only Medicare beneficiaries. Five studies assessed the relationship between SEP-1 implementation and sepsis mortality; only 1 showed significant benefit, but it did not adjust for mortality trends before SEP-1 implementation. All 17 studies were observational, and none had low risk of bias.

LIMITATIONS: The conclusions are limited by the underlying quality of the available studies, as all were observational. Because there was considerable methodologic heterogeneity among the included studies, a meta-analysis was not performed as the results could have been misleading.

CONCLUSION: This review found no moderate- or high-level evidence to support that compliance with or implementation of SEP-1 was associated with sepsis mortality. CMS should reconsider the addition of SEP-1 to the Hospital VBP Program.

PRIMARY FUNDING SOURCE: None. (PROSPERO: CRD42023482787).

PMID:39961104 | DOI:10.7326/ANNALS-24-02426

Tree Physiol. 2025 Feb 17:tpaf023. doi: 10.1093/treephys/tpaf023. Online ahead of print.

ABSTRACT

Droughts during dry seasons may pose a greater threat to Mediterranean forests under climate change. Effective desiccation avoidance strategies include reduced water loss rates, enhanced tissue water storage capacity, and greater root water access, which can avoid or delay dehydration damage. However, resource allocation competition may lead to trade-offs among these strategies that are not yet fully understood. In this study, six woody species from a Mediterranean forest were selected. We measured their twig hydraulic capacitance, ranging from 0.32-2.81 mmol m-2 MPa-1, to assess tissue water storage capacity, and twig residual conductance (gres) at 25 °C, ranging from 1.23-7.73 mmol m-2 s-1, to evaluate water loss rate. We found that the leaves of all four evergreen Mediterranean species featured sunken or hidden stomata, which may contribute to their low gres. The gres was also measured across a 25 °C-30 °C-40 °C temperature gradient, revealing species-specific response patterns. Predawn water potential (ΨPD) and the difference between predawn and midday water potential (∆Ψ) at the end of the dry summer season were used to estimate root water access. Significant trade-offs in plant desiccation avoidance strategies were observed as gres positively correlated with ∆Ψ (R2 = 0.78, P = 0.02) and twig hydraulic capacitance negatively correlated with ΨPD (R2 = 0.68, P = 0.04). Consequently, species with greater root water access exhibited lower tissue water storage capacity and higher gres, potentially increasing their mortality risk during extreme droughts when soil moisture is unavailable. By inverting a plant desiccation model, we demonstrated that both the calculated minimum hydraulic capacitance required for daily plant survival and a novel risk index positively correlated with ΨPD, supporting this conclusion. Notably, these findings align with historical statistics of tree mortality. Additionally, the risk index increased under scenarios of elevated temperature.

PMID:39961024 | DOI:10.1093/treephys/tpaf023