Nevin Manimala

Med Vet Entomol. 2025 Jul 14. doi: 10.1111/mve.12823. Online ahead of print.

ABSTRACT

As a tropical country, Colombia hosts a wide range of arthropods that can act as vectors of disease-causing pathogens, particularly those carrying hemopathogens. Ticks play a crucial role in the transmission of zoonotic pathogens, impacting both human and veterinary health. The pathogen load of ticks from wildlife is of particular concern, as it can contribute to the spillover of infectious agents to domestic animals and humans, highlighting the need for surveillance and control strategies to mitigate emerging tick-borne diseases. Therefore, this study aimed to determine the presence of microorganisms in ticks collected from wildlife in Antioquia (Colombia) through bioinformatic analysis. A prospective, cross-sectional, random, non-probabilistic, convenience-based study involving tick collection from animals in three different zones of Antioquia was conducted. Initially, vertebrate species were morphologically characterized via taxonomic keys and identification guides for amphibians, reptiles, birds, and mammals. Ticks were manually collected from these animals and preserved in absolute ethanol for later taxonomic identification. Genomic DNA was then extracted, and the resulting reads were processed through bioinformatic analysis, achieving taxonomic classification within DNA libraries of gram-positive bacteria, gram-negative bacteria, and parasites. Additionally, descriptive statistics were calculated for all variables of interest at the animal level (e.g., genus, species, sex, and age group, when applicable) and study zone. A total of 570 ticks, predominantly Amblyomma spp., were obtained from 46 host animals. Ticks from lizards presented the highest bacterial richness and diversity (based on 16S gDNA), whereas ticks from amphibians presented the lowest. Proteobacteria dominated most samples, as shown by taxonomic composition at the phylum, family, and genus levels. Ticks collected from mammals displayed lower diversity and richness than those collected from reptiles. For parasitic communities (18S gDNA), dominant eukaryotes were identified in ticks from mammals, excluding host-related taxa. Overall, lizard-associated ticks presented the most complex microbial diversity, whereas amphibian ticks were less diverse, highlighting the significant variation in microbial and parasitic communities across host species. This study highlights the microbial diversity of ticks from wild hosts in Colombia, focusing on the dominance of Francisella, Rickettsia, Aspergillus, and Penicillium. These findings underscore the need for further research on their ecological roles, transmission dynamics, and potential health risks, aiming to inform strategies to mitigate tick-borne diseases.

PMID:40658399 | DOI:10.1111/mve.12823

J Chem Inf Model. 2025 Jul 14. doi: 10.1021/acs.jcim.5c00893. Online ahead of print.

ABSTRACT

Molecular docking is a widely used technique in structure-based drug design for generating poses of small molecules in a protein receptor structure. These poses are then ranked to prioritize compounds for experimental validation. Numerous approaches to assessing the structural fit of a ligand exist, ranging from simple scoring functions to more elaborate free energy calculations. Regardless of the prioritization method chosen, its accuracy is limited by the quality of the protein-ligand pose. Here, we apply two established statistical approaches for quantifying atomic interaction preferences and torsional ligand strain, respectively, to compare poses generated by the docking algorithm Vina with crystallographic data from the PDB and CSD. This analysis allows us to identify potential deficiencies in the docking algorithm, such as underestimated electrostatic repulsion or high-energy hydroxyl conformations. By highlighting such inaccuracies, we aim to inspire improvements in future docking algorithms. Finally, a pose scoring approach is proposed that significantly improves the retrieval of the experimental pose from a set of docked poses.

PMID:40658398 | DOI:10.1021/acs.jcim.5c00893

Stat Med. 2025 Jul;44(15-17):e70111. doi: 10.1002/sim.70111.

ABSTRACT

Data collection procedures are often time-consuming and expensive. An alternative to collecting full information from all subjects enrolled in a study is a two-phase design: Variables that are inexpensive or easy to measure are obtained for the study population, and more specific, expensive, or hard-to-measure variables are collected only for a well-selected sample of individuals. Often, only these subjects that provided full information are used for inference, while those that were partially observed are discarded from the analysis. Recently, semiparametric approaches that use the entire dataset, resulting in fully efficient estimators, have been proposed. These estimators, however, have challenges incorporating multiple covariates, are computationally expensive, and depend on tuning parameters that affect their performance. In this paper, we propose an alternative semiparametric estimator that does not pose any distributional assumptions on the covariates or measurement error mechanism and can be applied to a wider range of settings. Although the proposed estimator is not semiparametric efficient, simulations show that the loss of efficiency to estimate the parameters associated with the partially observed covariates is minimal. We highlight the estimator’s applicability to real-world problems, where data structures are complex and rich, and complicated regression models are often necessary.

PMID:40658389 | DOI:10.1002/sim.70111

Adv Wound Care (New Rochelle). 2025 Jul 14. doi: 10.1177/21621918251359558. Online ahead of print.

ABSTRACT

Objective: To investigate the effectiveness of real-time fluorescence imaging (RTFI)-assisted debridement in managing chronic wounds compared with standard surgical debridement. Approach: This study was a patient-blinded, randomized clinical trial conducted from February 17, 2021, to July 30, 2021, on patients with chronic wounds. Patients were randomized to an RTFI group (M group) or conventional group (C group). The primary outcomes were as follows: percentage of residual bacterial area (preoperative and postoperative), number of debridements, high-quality debridement ratio, operation duration, and wound healing duration. Results: A total of 100 patients were enrolled in both groups. No significant difference in the percentage of preoperative residual bacterial area or high-quality debridement ratio was seen. The M group underwent debridement an average of 2.6 times and had a significantly longer duration of operation (33.5 ± 12.7 min) than the C group (29.9 ± 10.4 min; p = 0.031). The postoperative residual bacterial area was significantly lower in the M than in the C group (6.83% ± 1.39% vs. 30.0% ± 12.37%, respectively; p < 0.001). The M group required significantly fewer wound healing days (49.2 ± 25.3 vs. 63.0 ± 27.9, p < 0.001). Secondary outcomes also demonstrated statistically significant differences in total hospitalized days (17.5 ± 9.3 vs. 21.5 ± 12.5, p < 0.01), days of antibiotic use (15.5 ± 8.7 vs. 18.7 ± 6.7, p < 0.01), and reinfection rates (4 of 100 vs. 22 of 100, p < 0.001). Innovation: RTFI can detect signals from normal skin components and bacterial metabolites. Therefore, interpretation of RTFI results should be correlated with the clinical condition. RTFI is associated with high-quality debridement. This technique can also be applied in targeted biopsy and in training young staff to mature debridement procedures. Conclusion: RTFI in debridement is associated with favorable clinical outcomes and may have a positive influence on chronic wound healing.

PMID:40658376 | DOI:10.1177/21621918251359558

Stat Med. 2025 Jul;44(15-17):e70143. doi: 10.1002/sim.70143.

ABSTRACT

Mendelian randomization (MR) uses genetic variants as instrumental variables to infer causal effects of exposures on an outcome. One key assumption of MR is that the genetic variants used as instrumental variables are independent of the outcome conditional on the risk factor and unobserved confounders. Violations of this assumption, that is, the effect of the instrumental variables on the outcome through a path other than the risk factor included in the model (which can be caused by pleiotropy), are common phenomena in human genetics. Genetic variants, which deviate from this assumption, appear as outliers to the MR model fit and can be detected by the general heterogeneity statistics proposed in the literature, which are known to suffer from overdispersion, that is, too many genetic variants are declared as false outliers. We propose a method that corrects for overdispersion of the heterogeneity statistics in uni- and multivariable MR analysis by making use of the estimated inflation factor to correctly remove outlying instruments and therefore account for pleiotropic effects. Our method is applicable to summary-level data.

PMID:40658369 | DOI:10.1002/sim.70143

Trop Anim Health Prod. 2025 Jul 14;57(6):300. doi: 10.1007/s11250-025-04565-7.

ABSTRACT

OBJECTIVE: The objective of this study is to investigate the presence of major genes affecting body weight in hair goats. The application of Bayesian segregation analysis to big data facilitates more precise identification of intricate genetic structures and variations. This approach offers more profound biological insights through the detection of concealed genetic elements within big datasets. The precise quantification of additive genetic effects is fundamental for achieving sustainable genetic progress through targeted selection. Furthermore, the evaluation of dominance effects offers critical insights into heterozygote advantage, elucidating the mechanisms underlying heterosis and resilience in growth-related traits within livestock populations.

METHODS: To rapidly and accurately identify the presence of major genes, pedigree data and phenotypic data were employed in a Bayesian segregation analysis. For this purpose, 4072 records of body weight were analysed, measured at two different time points (birth weight (Time1) and body weight measured at approximately 100-120 days of age (Time2)). The data set comprised 2036 animals (n = 1038 male, n = 998 female). Gibbs sampling was employed to make statistical inferences regarding posterior distributions. These inferences were based on 20 replications of the Markov chain for each trait, with 100,000 samples collected, with each 500th sample retained due to the high correlation among the samples.

RESULTS: In this study, the estimated error variance, major gene variance, polygenic variance, dominance effect, and additive genetic effect were determined through Bayesian segregation analysis. The dominance effect (-1.797) was found to be smaller than the additive genetic effect (3.594) for birth weight, whereas for body weight at 4 months of age, the dominance effect (55.902) was found to be higher than the additive genetic variance (54.988). The polygenic and major gene heritabilities were estimated to be 0.51 (± 0.56) and 0.81 (± 0.91) for body weight, and 0.44 (± 0.55) and 0.86 (± 0.93) for body weight at four months of age, respectively.

CONCLUSION: The results of this study indicate that the 95% highest posterior density regions (HPDs) for the major gene parameter, particularly for the major gene variance, do not include 0, indicating the statistical significance of the major gene component.

PMID:40658343 | DOI:10.1007/s11250-025-04565-7

Clin Drug Investig. 2025 Jul 14. doi: 10.1007/s40261-025-01462-7. Online ahead of print.

ABSTRACT

BACKGROUND: Dapagliflozin and empagliflozin are emerging as promising treatment options for diabetic kidney disease (DKD).

OBJECTIVE: This study sought to evaluate the cost effectiveness of incorporating dapagliflozin and empagliflozin into the standard treatment for DKD in China.

METHODS: A Markov model was constructed to evaluate the cost-effectiveness of dapagliflozin and empagliflozin plus standard treatment versus standard treatment alone for DKD treatment from a healthcare perspective. Costs and utility data was obtained from published literatures within the Chinese context. The primary outcome included total cost, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratio (ICER). GDP per capita of 2023 in China (¥89,358) was utilized as the willingness-to-pay threshold.

RESULTS: Compared to standard treatment alone, add-on therapy of dapagliflozin or empagliflozin resulted in a higher total cost than those solely receiving standard treatment (+¥19,203.56 and +¥9496.92, respectively). However, both dapagliflozin and empagliflozin also yielded more life-years (+1.72 vs. +1.40) and QALYs (+1.40 vs. +0.88). The ICER per life-year and ICER per QALY was ¥11,178.52 and ¥18,192.50 for dapagliflozin and ¥6773.10 and ¥10,811.64 for empagliflozin, respectively. The incremental net monetary benefit was ¥75,120.54 and ¥68,994.90 for dapagliflozin and empagliflozin, respectively. Sensitivity analysis supported the main findings of the base-case analysis as the cost-effectiveness of dapagliflozin or empagliflozin was sustained for most plausible ranges of parameter values.

CONCLUSIONS: Considering that the ICER falls below the predefined willingness-to-pay threshold, incorporating dapagliflozin and empagliflozin into standard treatment for DKD is likely to be a cost-effective strategy in China.

PMID:40658333 | DOI:10.1007/s40261-025-01462-7

CJEM. 2025 Jul 14. doi: 10.1007/s43678-025-00958-7. Online ahead of print.

ABSTRACT

OBJECTIVES: Early Pregnancy Assessment Clinics provide gold-standard care to patients experiencing complications of early pregnancy, but their impact on emergency department (ED) volumes and consultation practices are largely unknown. The primary objective was to assess the volume of patients experiencing complications of early pregnancy presenting to the ED before and after the opening of an Early Pregnancy Assessment Clinic in Saskatoon, Saskatchewan. Secondary outcomes included inpatient prescribing practices and evaluation of Early Pregnancy Assessment Clinic referral patterns.

METHODS: We performed a health records review including all patients presenting to 3 Saskatoon-area EDs in the 6 months before and after the Early Pregnancy Assessment Clinic opening and examined all referrals to the center in the first 6 months of its opening. Charts were excluded if patients were directly presenting for a specialist service, were admitted, and were presenting with complications unrelated to fetal outcomes. We calculated descriptive statistics and compared using z tests.

RESULTS: We identified 1242 charts, of which 757 met eligibility criteria. There were 393 visits pre-opening and 364 visits post-opening. However, only 33% of eligible patients were referred to the Early Pregnancy Assessment Clinic in the 6-month period after it was opened. Direct referrals to obstetrics decreased 39.9% from 20.1% to 12.1% (p = 0.002).

CONCLUSIONS: While patient visits were only moderately reduced and return visits were the same in the pre- and post- opening periods, the number of inpatient consults to obstetrics and gynecology were significantly reduced. This is clinically important in reducing the burden of in-hospital consults and allowing for greater flow through the ED while providing patient-centered care.

PMID:40658317 | DOI:10.1007/s43678-025-00958-7

Eur J Epidemiol. 2025 Jul 14. doi: 10.1007/s10654-025-01277-y. Online ahead of print.

ABSTRACT

While previous literature suggests that plant-based diets may be associated with a lower risk of breast cancer, evidence remains inconsistent. In this study, we investigated the association between adherence to plant-based diets and breast cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Overall plant-based diet index (PDI), healthful (hPDI), and unhealthful PDI (uPDI) were calculated, and multivariable Cox models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) of breast cancer for the three indices. Mediation analysis was performed to assess the role of body mass index (BMI) and waist circumference (WC) in the association between hPDI and postmenopausal breast cancer risk. Over a median follow-up of 14.9 years, 10,805 incident invasive breast cancer cases were identified among 258,343 women. In the multivariable model, not adjusted for BMI, higher adherence to hPDI was inversely associated with breast cancer risk, with HR per 1-SD increase [95% (CI)] of 0.97 (0.94, 0.99). The corresponding HRs (95% CI) per 1-SD increase for overall PDI and uPDI were 0.98 (0.96, 1.00) and 1.01 (0.99, 1.03), respectively. The associations between hPDI and postmenopausal breast cancer were partly explained by BMI and WC, which mediated 30% and 52% of this association, respectively. Higher adherence to hPDI was associated with a slightly lower total breast cancer risk. For postmenopausal breast cancer, this association was partly explained by lower BMI or WC. These findings suggest that promoting healthful plant-based diets could support breast cancer risk reduction.

PMID:40658296 | DOI:10.1007/s10654-025-01277-y

Radiol Phys Technol. 2025 Jul 14. doi: 10.1007/s12194-025-00935-w. Online ahead of print.

ABSTRACT

Trigeminal neuralgia (TN) is characterized by severe facial pain and is treated with medications, surgery, percutaneous procedures, and stereotactic radiosurgery (SRS). The Gamma Knife (GK) has historically been the gold standard for SRS in TN, with alternatives such as the CyberKnife (CK) and standard linear accelerator (LA) having recently emerged. This study compared GK, CK, and LA treatments for TN via dosimetric analysis. Twenty patients (10 right- and 10 left-sided) with TN were planned in the three modalities. Dosimetric parameters, including D_Max, D_Min, D_Mean, D_98%, D_90%, D_50%, D_30%, and V_4Gy, were evaluated. The statistical significance was assessed using paired t tests. The CK and LA plans achieved a 60 Gy target coverage comparable to the GK plan. The GK plan exhibited superior brain stem sparing and lower V_4Gy compared with CK (p = 0.0013) and LA (p = 0.0001). Significant differences in D_Min, D_98%, D_90%, D_50%, and D_30% were observed between GK and CK (p < 0.05) and GK and LA (p < 0.05), but not for the CK-LA comparisons. The brain stem dose parameters (D_{0.03 cc}, D_1%, and D_2%) were significantly lower in the GK plan (p < 0.05). The GK exhibited better normal tissue sparing and brain stem dose distribution than CK and LA, attributable partly to its higher beam count. CK and LA require more intricate planning times. Despite the established efficacy of GK, CK and LA offer viable alternatives, underscoring the need for further research on the clinical outcomes of TN treatment in the respective modalities.

PMID:40658293 | DOI:10.1007/s12194-025-00935-w