Nevin Manimala

Mol Biol Evol. 2025 May 26:msaf117. doi: 10.1093/molbev/msaf117. Online ahead of print.

ABSTRACT

Efficient and accessible analysis of genome-wide single nucleotide polymorphism (SNP) data is vital for advancing molecular biology, evolutionary genetics, and breeding research. However, current analytical pipelines are often fragmented and require command-line expertise, limiting accessibility for many researchers. Here, we present ShiNyP, an interactive R/Shiny platform that integrates all popular SNP analysis modules within a single and intuitive user interface, supporting the entire workflow from data import and quality control to population structure inference, diversity analysis, selective scan, and core collection. ShiNyP accommodates datasets from haploid, diploid, and polyploid species and automates the generation of over 70 publication-ready visualizations and summary tables. A distinctive feature is its automated report module, which employs generative AI to deliver structured, interpretable narratives of complex statistical results. Performance benchmarks demonstrate that ShiNyP efficiently processes large-scale datasets on standard hardware. The ShiNyP platform is freely available at https://github.com/TeddYenn/ShiNyP, providing an efficient, reproducible, and user-friendly solution for population genomics research.

PMID:40418736 | DOI:10.1093/molbev/msaf117

J Med Internet Res. 2025 May 26;27:e70665. doi: 10.2196/70665.

ABSTRACT

BACKGROUND: As the second most common neurological disorder, epilepsy requires long-term management to ensure better seizure control and improved patient outcomes. Health education and sustained care significantly help people with epilepsy manage their condition effectively. Internet hospitals (IHs) have emerged as a promising approach to enhancing health care accessibility. These digital platforms can significantly improve the quality of life for patients with epilepsy. However, despite their growing adoption, research on the application of IHs in the follow-up management of epilepsy remains limited, highlighting the need for further investigation.

OBJECTIVE: This study has 2 primary aims. The first aim was to assess and compare the differences in quality of life, anxiety, and depression between IH follow-up and traditional outpatient follow-up for patients with epilepsy. The second aim was to explore chronic disease management models that are tailored to meet the needs of patients with epilepsy, improving their overall care.

METHODS: Eligible patients diagnosed with epilepsy were recruited at Sichuan Provincial People’s Hospital and randomly assigned to the intervention or control group. Data collected included demographic information, clinical characteristics, and scores from the Quality of Life in Epilepsy-31 (QOLIE-31), Generalized Anxiety Disorder-7 Scale (GAD-7), and Neurological Disorders Depression Inventory for Epilepsy (NDDI-E). The control group received traditional outpatient follow-up, while the intervention group was managed via the IH. Both groups received epilepsy health education. After 6 months, changes in quality of life, anxiety, and depression were assessed using the same scales. Data analysis followed the intention-to-treat principle, and a linear mixed model was used to examine the intervention effect on primary and secondary outcomes. The effect sizes of group differences were calculated using Hedges g (0.2-0.4: small, 0.5-0.7: medium, and ≥0.8: large).

RESULTS: A total of 214 patients with epilepsy participated in the study (intervention group: N=107; control group: N=107). At the end of the study, 94.4% (101/107) in the intervention group and 93.5% (100/107) in the control group had completed the follow-up visits. After the intervention, the intention-to-treat analysis revealed evidence for improved quality of life (QOLIE-31 total score; F_216.53=13.10, P<.001) with small between-group effects (Hedges g=0.49, 95% CI 0.22-0.76) in favor of the intervention group. We also found evidence of reduced depression, as well as improved seizure worry, overall quality of life, emotional well-being, energy or fatigue, medication side effects, with effects ranging from small to medium (Hedges g=0.42-0.79).

CONCLUSIONS: Long-term follow-up through IHs can effectively improve the quality of life and reduce anxiety and depression in patients with epilepsy. This model provides effective support, making it an important tool for managing epilepsy. Therefore, IH management is recommended as a feasible approach for epilepsy follow-up in clinical practice.

TRIAL REGISTRATION: Chinese Clinical Trial Registry ChiCTR2500101061; https://www.chictr.org.cn/showprojEN.html?proj=260855.

PMID:40418570 | DOI:10.2196/70665

JMIR Res Protoc. 2025 May 26;14:e60675. doi: 10.2196/60675.

ABSTRACT

BACKGROUND: Despite the availability of vaccines, immunocompromised patients are still at high risk for severe COVID-19. Vaccination has been proven to be an effective measure in preventing severe SARS-CoV-2 infections; however, data on B- and T-cell responses are lacking. While vaccination schedules for the general population have been defined, achieving immunogenicity in patients who are immunocompromised remains a challenge.

OBJECTIVE: The primary objective is to analyze anti-spike-immunoglobulin G (IgG) titers after repeated messenger ribonucleic acid vaccinations in patients who are immunocompromised. Further objectives are to analyze data on humoral immune responses and to evaluate data on cellular immune responses.

METHODS: This multicenter, prospective, noninterventional study aims to determine the immunogenicity and reactogenicity of an implemented standard-of-care COVID-19 vaccination strategy in patients who are immunocompromised. A total of 100 patients will be recruited at three study sites. Patients are eligible for study inclusion when they are 18 years or older, vaccinated according to the recent version of the COVID-19 vaccination standard, and if the patient is immunocompromised according to stage 3 of the classification “Stages of Immunosuppression.” The study analyzes B- and T-cell responses generated within the standard-of-care COVID-19 vaccination strategy. Additional blood samples will be drawn at each scheduled outpatient visit. Study-related blood samples will be used to extract ethylenediaminetetraacetic acid plasma and peripheral blood mononuclear cells for evaluation of B- and T-cell responses to COVID-19 vaccinations. For this study, no additional visits or invasive procedures will be performed in addition to standard care.

RESULTS: As of August 2024, the study has enrolled 32 patients. The recruitment phase is still ongoing.

CONCLUSIONS: Results will be used to optimize vaccination and booster schedules for patients who are immunocompromised and to increase rates of protection against severe SARS-CoV-2 infections. Further, results may identify risk and treatment factors, which lead to low immune responses in patients vaccinated against COVID-19, as well as the impact of repeated vaccination on B- and T-cell responses.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05597761; https://clinicaltrials.gov/study/NCT05597761.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/60675.

PMID:40418566 | DOI:10.2196/60675

Front Nutr. 2025 May 9;12:1482719. doi: 10.3389/fnut.2025.1482719. eCollection 2025.

ABSTRACT

INTRODUCTION: The influence of artificially sweetened beverages (ASBs) on metabolic risk factors for non-communicable diseases (NCDs) remains unclear. This study aimed to systematically review the literature concerning whether the effects of ASBs on body weight and metabolic risk factors are equivalent to those of unsweetened beverages (USBs).

METHODS: We searched PubMed, Embase, Web of Science, and Cochrane Library databases from their establishment until March 3, 2025. Only randomized controlled trials (RCTs) comparing ASBs and USBs were included. Literature screening, data extraction, and bias evaluations were performed. Statistical analyses were performed using Review Manager 5.4 and Stata 15.0 software.

RESULTS: Nine RCTs involving 1,457 individuals were included. Meta-analysis findings indicated no statistically significant differences between ASB and USB groups in terms of weight, waist circumference, fasting blood glucose, glycated hemoglobin, homeostatic model assessment for insulin resistance, total cholesterol, triglycerides, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, systolic blood pressure, and diastolic blood pressure (all p > 0.05).

CONCLUSION: The study findings do not support the hypothesis that ASBs pose significant risks or benefits in terms of metabolic risk factors for NCDs. However, given this study applied a heterogeneous ASB formula, it could not adequately consider the role of specific artificial sweeteners. Further research is needed to evaluate the potential effect of different artificial sweeteners and their doses on health.

SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk, identifier CRD420251027794.

PMID:40416387 | PMC:PMC12098100 | DOI:10.3389/fnut.2025.1482719

Front Nutr. 2025 May 9;12:1544338. doi: 10.3389/fnut.2025.1544338. eCollection 2025.

ABSTRACT

BACKGROUND: Nutritional risk is a significant concern for patients undergoing peritoneal dialysis (PD), adversely affecting their quality of life and increasing the risk of infections and complications. Effective screening tools are needed to identify high-risk patients for targeted interventions. This study investigates whether different nutritional assessment methods, like the Controlling Nutritional Status (CONUT) score and Nutritional Risk Index (NRI), correlate with patient prognosis, highlighting the importance of selecting appropriate screening tools to improve clinical outcomes in PD patients.

METHODS: This multicenter retrospective cohort study initially collected data from 2,427 patients across 10 centers, but ultimately included a cohort of 2,105 PD patients to evaluate the prevalence of malnutrition assessed using both the CONUT and NRI and its independent effects on all-cause mortality. Statistical analyses included log-rank tests, Cox regression models and the receiver operating characteristic curves to evaluate the association between nutritional risk and mortality.

RESULTS: Our findings revealed that 76.58% of patients were classified as having nutritional risk according to the CONUT score, while 79.10% by the NRI. Patients with nutritional risk exhibited a significantly higher all-cause mortality rate (log-rank test, p < 0.001). Cox regression analysis demonstrated that severe nutritional risk was an independent predictor of all-cause mortality, with adjusted hazard ratios of 2.55 (95% CI, 1.34-4.85; p = 0.007) for the CONUT score and 2.64 (95% CI, 1.74-4.03; p < 0.001) for the NRI. Kaplan-Meier survival curves highlighted the correlation between nutritional risk and survival.

CONCLUSION: CONUT and NRI are effective for initial nutritional risk screening in PD patients, enabling clinicians to identify risk individuals who should undergo diagnostic assessments for a more comprehensive nutritional evaluation. Their simplicity and ease of implementation support integration into routine practice, making it feasible for healthcare providers to conduct regular screenings. Future studies should validate dynamic monitoring approaches.

PMID:40416383 | PMC:PMC12098072 | DOI:10.3389/fnut.2025.1544338

Front Nutr. 2025 May 9;12:1590137. doi: 10.3389/fnut.2025.1590137. eCollection 2025.

ABSTRACT

BACKGROUND AND OBJECTIVES: Malnutrition is a common problem among cancer patients, significantly impacting clinical outcomes and quality of life. This study aimed to evaluate the prevalence of malnutrition and its associated factors in geriatric cancer patients undergoing chemotherapy.

MATERIALS AND METHODS: This prospective study included 471 patients aged 65 years and older, conducted at Ankara Etlik City Hospital between January and December 2023. Patients’ demographic, clinical, and nutritional statuses were assessed using the Mini Nutritional Assessment (MNA). Nutritional status was classified as normal (MNA ≥ 24), at risk of malnutrition (MNA 17-23.5), and malnourished (MNA < 17). Depression and insomnia were evaluated using the Geriatric Depression Scale (GDS) and the Insomnia Severity Index (ISI), respectively. Factors associated with malnutrition were analyzed statistically.

RESULTS: Malnutrition was identified in 20.5% of the patients. Malnutrition was significantly associated with radiotherapy (p = 0.001), surgical history (p = 0.001), adjuvant therapy (p = 0.002), metastatic disease (p = 0.011), low BMI (p < 0.001), high depression scores (p < 0.001), moderate-to-severe insomnia (p < 0.001), and the presence of comorbidities (p = 0.022). However, no significant association was found between pain and malnutrition (p = 0.07).

CONCLUSION: This study highlights the multifactorial nature of malnutrition in geriatric cancer patients and emphasizes the importance of regular nutritional assessments using validated tools like MNA. Early detection and intervention can improve clinical outcomes and quality of life. However, the study has certain limitations, including being single-center, the use of self-reported measures, and the exclusion of palliative patients, which may affect the generalizability of the results.

PMID:40416373 | PMC:PMC12101082 | DOI:10.3389/fnut.2025.1590137

Acta Radiol Open. 2025 May 22;14(5):20584601251342312. doi: 10.1177/20584601251342312. eCollection 2025 May.

ABSTRACT

BACKGROUND: Pericoronary adipose tissue density (PCAT) is a parameter that quantifies inflammation and atherosclerosis around the coronary arteries.

PURPOSE: To investigate the correlation between PCAT and plaque features, stenosis degrees in coronary arteries (LAD, RCA, Cx) with stenotic vulnerable plaques.

MATERIAL AND METHODS: A Retrospective study including 103 patients (64M, 39F) who underwent coronary computed tomography was retrospectively examined at a single center. PCAT and high-risk plaques were measured independently and compared to stenosis and coronary artery type. Adipose tissue attenuation, ranging from -180 to -25 HU, was measured along the plaque’s length and in a 0.5-1 mm region around the perilesional coronary arteries.

RESULTS: The PCAT values increases with the degree of stenosis in the LAD, Cx, and RCA (r = 0.9161, p < .001; r = 0.9717, p < .001; r = 0.9315, p < .001, respectively). PCAT values demonstrate a positive pattern when plaque length increases in all coronary arteries (r = -0.6316, p < .001; r = -0.8825, p < .001; r = -0.7529, p < .001; LAD, Cx, RCA). PCAT values differed significantly based on plaque type in all coronary arteries. Calcified plaques showed statistically significant differences compared to both soft and mixed plaques (p < .05). Patients with positive remodeling had PCAT values of -69.43 (±8.76) HU, while cases without positive remodeling had PCAT values of -84.54 (±7.65) HU, indicating a significant difference (p < .05).

CONCLUSION: The combined evaluation of plaque features, stenosis degree, and PCAT provides a more accurate prediction of possible acute coronary syndrome cases than analyzing stenosis degree alone.

PMID:40416366 | PMC:PMC12099116 | DOI:10.1177/20584601251342312

Can Pharm J (Ott). 2025 May 22:17151635251332612. doi: 10.1177/17151635251332612. Online ahead of print.

ABSTRACT

BACKGROUND: The World Health Organization’s right to health underscores the need for accessible, acceptable, and quality health services. Given that most Canadians use the Internet for health information, the readability of online pharmacy services information is crucial for accessibility.

METHODS: This study assessed the readability of online information about pharmacy services from Canadian provincial pharmacy regulatory authorities (PRAs) and community pharmacy banners. Public-facing website content was evaluated using various readability tests. Scores were compared to recommended reading grade levels by health organizations, and differences between PRA and community pharmacy banner websites were analyzed.

RESULTS: Website content from 9 PRAs and 10 community pharmacy banners was analyzed in June 2024. Average readability scores exceeded the recommended eighth-grade level, with summary scores ranging from 8.45 to 15.28. International English Language Testing System scores for all websites also surpassed reading benchmarks necessary for Canadian immigration. Mann-Whitney U tests indicated statistically significant differences between PRA and community pharmacy banner websites, with the latter being more readable.

DISCUSSION: The results suggest that both PRAs and community pharmacy banners provide information at an advanced reading level, hindering accessibility. This aligns with other research indicating that online health information is often too complex for the general public. Improving readability, particularly for new Canadians, is essential for better accessibility.

CONCLUSION: Public health information on PRA and community pharmacy banner websites generally exceeds the recommended readability level, limiting accessibility. Implementing readability assessments and plain-language standards can enhance the accessibility and engagement of online health information.

PMID:40416341 | PMC:PMC12098308 | DOI:10.1177/17151635251332612

J Mark Access Health Policy. 2025 May 9;13(2):21. doi: 10.3390/jmahp13020021. eCollection 2025 Jun.

ABSTRACT

Advances in primary healthcare coverage for the improvement in health outcomes at the population level comprise a major goal of public policies of health, particularly considering increases in hospitalization costs linked to chronic diseases in recent decades. Previous evidence shows the positive effects of access to primary healthcare on hospitalization indicators in high-income countries; however, there is a lack of literature on the subject in Latin American countries. Thus, the present study proposes a quantitative investigation on connections between primary healthcare quality and effectiveness in relation to hospitalization indicators, in addition to the identification of its effects on inequalities in hospitalizations in Brazil. The study was based on an empirical analysis of data from five cross-sectional surveys representative at the population level conducted by the Brazilian Institute for Geography and Statistics (IBGE) in 1998, 2003, 2008, 2013, and 2019. Information on the demographic, socioeconomic, and health characteristics of individuals compatible across surveys were included in the analyses, in addition to data on household and survey characteristics. The statistical analyses were based on the estimation of logistic regression models for the exploration of effects of primary healthcare quality and effectiveness on hospitalizations, inpatient days, and perception of quality of hospital care. Furthermore, the estimation of concentration indexes and their disaggregation allowed to verify trends and determinants of inequalities in hospitalization indicators in Brazil throughout the period. The results indicate that primary healthcare effectiveness is associated with the lower occurrence and frequency of hospitalizations, and a lower length of stay in hospitals. Primary healthcare quality was associated with the perception of higher quality of hospital care. Trends in hospitalization indicators showed reduction in inequalities towards low-income individuals from 1998 to 2013, and primary healthcare quality presented minor influence on inequalities in hospitalizations, inpatient days, and perception of quality of hospital care.

PMID:40416334 | PMC:PMC12101434 | DOI:10.3390/jmahp13020021

ACS Photonics. 2025 Apr 29;12(5):2291-2303. doi: 10.1021/acsphotonics.4c02430. eCollection 2025 May 21.

ABSTRACT

Combining multiple optical resonators or engineering dispersion of complex media has provided an effective method for demonstrating topological physics controlling photons in unprecedented ways such as unidirectional light propagation and spatially localized modes between an interface or on a corner. Further, adding nonlinear responses to those topological photonic systems has enabled achieving diverse phases of photons in both space and time, allowing for more functionalities in photonic devices that provide a new playground for studying dynamic features of nonlinear topological systems. However, most methods for describing nonlinear topological photonic systems rely on linear topological theories, making it challenging to accurately characterize the topology of nonlinear systems. Thus, substantial efforts have focused on rigorously describing nonlinear topological phases and developing effective tools to analyze nonlinear topological effects. Meanwhile, coupled multimode optical waveguides with nonlinear dynamic responses provide an excellent platform for the statistical description of photons, opening a new paradigm called “optical thermodynamics”. This review will introduce the basic concepts of nonlinear topological photonics and the recent development of theoretical approaches focusing on data-driven approaches for creating phase diagrams as well as the spectral localizer framework and the pseudospectrum method for understanding optical nonlinearities in topological systems. In addition, the new concept of optical thermodynamics will be introduced with some recent theoretical works.

PMID:40416326 | PMC:PMC12100720 | DOI:10.1021/acsphotonics.4c02430