Nevin Manimala

BMC Bioinformatics. 2025 Nov 25. doi: 10.1186/s12859-025-06215-z. Online ahead of print.

ABSTRACT

As data complexity and volume increase rapidly, efficient statistical methods for identifying significant variables become crucial. Variable selection plays a vital role in establishing relationships between predictors and response variables. The challenge lies in achieving this goal while controlling the False Discovery Rate (FDR) and maintaining statistical power. The knockoff filter, a recent approach, generates inexpensive knockoff variables that mimic the correlation structure of the original variables, serving as negative controls for inference. In this study, we extend the use of knockoffs to Light Gradient Boosting Machine (LightGBM), a fast and accurate machine learning technique. Shapely Additive Explanations (SHAP) values are employed to interpret the black-box nature of machine learning. Through extensive experimentation, our proposed method outperforms traditional approaches, accurately identifying important variables for each class. It offers improved speed and efficiency across multiple datasets. To validate our approach, an extensive simulation study is conducted. The integration of knockoffs into LightGBM enhances performance and interpretability, contributing to the advancement of variable selection methods. Our research addresses the challenges of variable selection in the era of big data, providing a valuable tool for identifying relevant variables in statistical modeling and machine learning applications.

PMID:41291416 | DOI:10.1186/s12859-025-06215-z

BMC Bioinformatics. 2025 Nov 25. doi: 10.1186/s12859-025-06276-0. Online ahead of print.

ABSTRACT

BACKGROUND: Reconstructing ECG signals from PPG measurements is a critical task for non-invasive cardiac monitoring. While several public ECG-PPG datasets exist, they lack the diversity found in image datasets, and the data collection process often introduces noise, making ECG reconstruction from PPG signals challenging even for advanced machine learning models.

RESULTS: We propose a novel ODE-based method for generating synthetic ECG-PPG pairs to enhance training diversity. Building on this, we introduce CLEP-GAN, a subject-independent PPG-to-ECG reconstruction framework that integrates contrastive learning, adversarial learning, and attention gating. CLEP-GAN achieves performance that matches or surpasses current state-of-the-art methods, particularly in reconstructing ECG signals from unseen subjects. Evaluation on real-world datasets (BIDMC and CapnoBase) confirms its effectiveness. Additionally, our analysis shows that demographic factors such as sex and age significantly impact reconstruction accuracy, emphasizing the importance of incorporating demographic diversity during model training and data augmentation.

CONCLUSIONS: Our method produces synthetic ECG-PPG pairs with RR interval distributions closely aligned with their real counterparts and shows strong potential to simulate diverse rhythms such as regular sinus rhythm (RSR), sinus arrhythmia (SA), and atrial fibrillation (AFib). Furthermore, CLEP-GAN demonstrates robust performance on both synthetic and real datasets, achieving near-perfect reconstruction in synthetic settings and competitive results on real data. These findings highlight CLEP-GAN’s promise for reliable, non-invasive ECG monitoring in clinical applications.

PMID:41291415 | DOI:10.1186/s12859-025-06276-0

World J Surg. 2025 Nov 25. doi: 10.1002/wjs.70160. Online ahead of print.

ABSTRACT

BACKGROUND/AIMS: The HALP score, a scoring method that has demonstrated effectiveness in inflammatory clinical conditions and is increasingly used in clinical practice, can be utilized to distinguish between complicated and uncomplicated cases of acute appendicitis. Additionally, it may serve as a reference for initiating medical treatment at an earlier stage.

MATERIALS AND METHODS: Patients who were diagnosed with acute appendicitis and operated on were included. Patients who underwent conventional open appendectomy and laparoscopic appendectomy as surgical procedures were examined retrospectively by scanning their files. Preoperative CBC and biochemistry values of the patients were recorded by scanning their files retrospectively. From here, preoperative hemoglobin-albumin-lymphocyte-platelet (HALP) Score [hemoglobin (g/L) × albumin (g/L) × lymphocyte count (/L)]/platelet count (/L)], neutrophil-lymphocyte ratio (NLR) [neutrophil count (/L)/lymphocyte count (/L)] and platelet-lymphocyte ratio (PLR) [platelet count (/L)/lymphocyte count (/L)] were calculated manually.

RESULTS: There were statistically significant differences between patients with and without complications in terms of preoperative WBC, neutrophil counts and lymphocyte counts in the preoperative period (p values; 0.015, < 0.006 and < 0.004, respectively). There was no statistically significant difference in terms of other preoperative blood values (p > 0.05). There was a statistically significant difference between the groups in terms of NLR, PLR, and HALP score calculated from preoperative CBC parameters.

CONCLUSION: HALP score is an important biomarker, like other biomarkers, in the early diagnosis of complications, initiating antibiotic therapy earlier, gaining time during transport, and preventing complications that may arise due to exacerbation of the disease.

TRIAL REGISTRATION: NCT07002671.

PMID:41291390 | DOI:10.1002/wjs.70160

J Cancer Res Clin Oncol. 2025 Nov 25;151(12):329. doi: 10.1007/s00432-025-06364-x.

ABSTRACT

BACKGROUND: The lncRNA FOXD3-AS1 shows abnormal expression in various tumors, but its role in prostate cancer (PCa) remains unclear.

OBJECTIVE: This study sought to examine FOXD3-AS1 expression patterns in PCa and its molecular role in regulating PEG10 through miR-491-5p.

METHODS: The methodological approach involved the application of RT-qPCR to determine the expression profiles of FOXD3-AS1, miR-491-5p, and PEG10 across PCa tissues and in vitro cell systems; subcellular localization analysis determined the cytoplasmic distribution of FOXD3-AS1; Cell proliferation, migratory and invasive capacities, as well as apoptosis, were assessed using CCK-8, transwell, and flow cytometric assays, respectively; dual-luciferase reporter assays verified the targeting relationships between molecules; statistical software was used for data analysis.

RESULTS: FOXD3-AS1 demonstrated substantial upregulation within prostate carcinoma tissues and cultured cells and was found to be predominantly localized within the cytoplasmic compartment. Functional experiments demonstrated that depleting FOXD3-AS1 strongly impeded cell multiplication, spread, and penetration, and enhanced apoptotic activity. Rescue assays demonstrated that co-intervention of miR-491-5p or its downstream target PEG10 could counteract the tumor-suppressive effects induced by FOXD3-AS1 silencing. Mechanistically, FOXD3-AS1 functions as a ceRNA, sequestering miR-491-5p to attenuate its repression of PEG10.

CONCLUSION: FOXD3-AS1 influences PCa cell behavior via the miR-491-5p/PEG10 axis.

PMID:41291383 | DOI:10.1007/s00432-025-06364-x

Nutr Clin Pract. 2025 Nov 25. doi: 10.1002/ncp.70075. Online ahead of print.

ABSTRACT

BACKGROUND: COVID-19 significantly affected traditional nutrition assessment methods, forcing experts to quickly adjust to new constraints. This study examined practices in clinical nutrition during the pandemic in Latin America based on professional background or experience.

METHODS: A cross-sectional survey from July to November 2021 involved clinical nutrition experts from 18 Latin American countries. A 70-item questionnaire assessed anthropometric, biochemical, and dietetic indicators; screening and diagnostic tools; and methods for estimating nutrient requirements. For statistical analyses we used nonparametric tests and latent profile analyses.

RESULTS: Among the 398 participants, the sample included dietitians/nutritionists (63%), physicians (25%), and nurses (12%). Biochemical indicators were used by 87%, dietetic indicators by 71%, and anthropometric measurements by 65%. Only one-third used GLIM criteria, whereas nearly 30% indicated that they did not use any screening tools. Variations in professional practices were observed regarding laboratory test requisitions and dietary assessment methodologies. Dietitians favored the use of recalls, whereas physicians generally ordered a greater number of biochemical tests. There was a significant variation in the estimation of protein and energy requirements, particularly outside of critical care environments. The influence of seniority on assessment practices was negligible.

CONCLUSION: Nutrition evaluation throughout the pandemic has demonstrated considerable variability with an individual’s profession demonstrating a more substantial impact than their level of seniority. The limited utilization of standardized tools highlights continued fragmentation and emphasizes the necessity for interprofessional education and institutional policies to ensure consistent, evidence-based nutrition care.

PMID:41291368 | DOI:10.1002/ncp.70075

Sports Med. 2025 Nov 25. doi: 10.1007/s40279-025-02346-8. Online ahead of print.

ABSTRACT

BACKGROUND: Soccer is a high-intensity sport that requires high levels of physical fitness, including balance, change of direction (CoD), speed and power. The FIFA 11 + program has been widely promoted to enhance physical fitness and reduce injury occurrence.

OBJECTIVE: This meta-analysis set out to examine how the FIFA 11 + program, implemented as a warm-up versus conventional warm-up (soccer-specific and alternative warm-ups), impacts physical fitness attributes in youth and adult soccer players.

METHODS: After a priori defined inclusion and exclusion criteria, 17 intervention studies with 611 male and female soccer players (Tier 2-4) aged 9-29 years were eligible to be included. The FIFA 11 + program implemented in the warm-up was contrasted with conventional warm-up programs (control) on outcome measures such as dynamic balance, CoD speed, linear sprint and proxies of muscle power (vertical jump height). The influence of potential moderators (e.g., training duration, frequency, session duration, age, sex, training and performance calibre) on study outcome measures was examined using subgroup analyses with the median split method.

RESULTS: Findings demonstrated small-to-moderate improvements in favour of FIFA 11 + compared with conventional warm-ups on dynamic balance (small standardized mean differences [SMDs] = 0.37, p < 0.001, heterogeneity [I²] = 7), CoD speed (moderate SMDs = – 0.65, p = 0.005, I² = 84), and vertical jump height (small SMDs = 0.56, p < 0.001, I² = 71). Results from the sub-analyses showed that, for dynamic balance, shorter training durations (< 9 weeks) produced larger effects than longer durations (≥ 9 weeks) (SMDs = 0.62 versus SMDs = 0.17). For vertical jump height, < 9 weeks also yielded greater improvements (SMDs = 0.79 versus SMDs = 0.26). In terms of weekly training frequency, ≥ 3 sessions/week elicited larger gains in change-of-direction speed (SMDs = – 1.05 versus SMDs = – 0.12) and vertical jump height (SMDs = 0.73 versus SMDs = 0.01) compared with < 3 sessions/week. Regarding participant characteristics, players aged ≥ 18 years showed greater improvements than those < 18 years in change-of-direction speed (SMDs = – 1.45 versus SMDs = – 0.06) and vertical jump height (SMDs = 0.64 versus SMDs = 0.22). For sex differences, males experienced greater benefits than females in change-of-direction speed (SMDs = – 0.79 versus SMDs = – 0.04) and vertical jump height (SMDs = 0.54 versus SMDs = 0.09). Finally, higher-level players (≥ tier 3) demonstrated greater improvements in vertical jump height than lower-tier players (< Tier 3) (SMDs = 0.75 versus SMDs = 0.01). The observed benefits were statistically significant but generally of small-to-moderate magnitude and affected by study heterogeneity and program implementation differences. Most studies included male participants, limiting generalizability to female and underrepresented populations. Several studies also lacked rigorous methodological design, particularly in allocation, concealment and blinding. Reporting of training and demographic variables was often incomplete. These limitations highlight the necessity for rigorously designed, low-bias randomized controlled trials with standardized implementation of the FIFA 11 + program and thorough reporting to enhance the reliability of causal conclusions and improve clinical interpretation.

CONCLUSION: The FIFA 11 + program was more effective than conventional soccer warm-up programs to enhance soccer players’ physical fitness (i.e., dynamic balance, CoD speed, vertical jump height). A shorter training duration (< 9 weeks) and more weekly training sessions (≥ 3 sessions/week) induced larger performance effects. FIFA 11 + was more effective in older (≥ 18 years) and male players and in players of higher performance calibre (≥ Tier 3). These findings underscore the versatility of the FIFA 11 + program to improve soccer players’ physical fitness, supporting its integration into the warm-up of regular soccer training sessions.

PROTOCOL REGISTRATION: https://www.crd.york.ac.uk/PROSPERO/view/CRD42025633810 , PROSPERO: CRD42025633810.

PMID:41291351 | DOI:10.1007/s40279-025-02346-8

J Bone Miner Metab. 2025 Nov 25. doi: 10.1007/s00774-025-01665-0. Online ahead of print.

NO ABSTRACT

PMID:41291339 | DOI:10.1007/s00774-025-01665-0

Langenbecks Arch Surg. 2025 Nov 26;411(1):19. doi: 10.1007/s00423-025-03914-2.

ABSTRACT

PURPOSE: Ventral hernias are frequently encountered in general surgery. In recent years, minimally invasive techniques, including the Extended View Totally Extraperitoneal Repair (eTEP), have gained popularity. Meta-analyses suggest that eTEP may offer both intraoperative and postoperative advantages over alternative approaches. This retrospective study aimed to evaluate intra- and postoperative complications, length of hospital stay, and the potential association between American Society of Anesthesiologists (ASA) Physical Status Classification and complication rates in patients who underwent eTEP. The findings may inform preoperative risk stratification and surgical planning based on ASA score.

METHODS: A monocentric, retrospective study of 95 patients who underwent eTEP for ventral hernia repair between January 2019 and December 2021 was conducted. Descriptive statistics and binary logistic regression analyses were performed to explore the association between the ASA score and perioperative complications.

RESULTS: Intraoperative complications occurred in 2.1% (n = 2), and postoperative complications were observed in 7.4% (n = 7). The median length of hospital stay was three days (IQR = 1). Logistic regression analysis did not identify a statistically significant association between the ASA score and the occurrence of either intra- or postoperative complications. Nonetheless, all observed complications arose in patients with ASA scores of ≥ II.

CONCLUSION: eTEP repair was associated with a low complication rate and short hospitalization. While ASA classification was not a statistically significant predictor of perioperative complications in this cohort, the absence of complications in ASA I patients suggests potential relevance. These findings highlight the need for larger, prospective studies to further evaluate the role of ASA classification in risk assessment for eTEP procedures.

PMID:41291335 | DOI:10.1007/s00423-025-03914-2

Surg Endosc. 2025 Nov 25. doi: 10.1007/s00464-025-12318-8. Online ahead of print.

ABSTRACT

INTRODUCTION: Parastomal hernia is a common and challenging complication after stoma formation, often requiring complex surgical management. To address limitations of conventional techniques, we developed the Hybrid Parastomal Endoscopic Repair (HyPER) technique, which combines laparoscopic and open approaches. This case series aimed to evaluate the long-term safety, efficacy, and technical considerations of the HyPER method in a large, consecutive cohort of patients.

METHODS: This retrospective, single-center case series included 200 consecutive patients treated between 2014 and 2024. Adult patients with symptomatic or recurrent parastomal hernias were included; exclusion criteria were severe comorbidities precluding surgery or lack of follow-up data. Demographic and operative variables, perioperative outcomes, and recurrence rates were analyzed. Descriptive statistics were used (mean, SD, range); no hypothesis testing was applied.

RESULTS: The majority of patients had EHS Type III or IV hernias. The mean operative time was 171 min. In 10% of cases, a cost-effective “Baldachin modification” using polypropylene mesh was employed. Stoma relocation was required in 87% of Type IV cases. Postoperative complications occurred in 12.5%, primarily wound infections. The recurrence rate was 5.5%, and quality of life significantly improved (VAS score increased from 3.15 to 9.15). No mortality was observed.

CONCLUSION: HyPER proved to be a safe and effective technique for treating parastomal hernias, especially in complex and recurrent cases. The approach allowed for thorough anatomical correction and yielded low recurrence rates with acceptable morbidity. The Baldachin modification may offer a viable low-cost alternative in resource-limited settings. Further multicenter studies are warranted to validate these findings and establish standardized protocols.

PMID:41291329 | DOI:10.1007/s00464-025-12318-8

Support Care Cancer. 2025 Nov 26;33(12):1134. doi: 10.1007/s00520-025-10182-9.

ABSTRACT

PURPOSE: Lorlatinib is the preferred first-line treatment for patients with ALK+ metastatic non-small cell lung cancer. However, this drug carries high rates of neurocognitive adverse events. This study further characterized these neurocognitive adverse events, examined risk factors, and, for the first time, explored social support as a mitigation strategy.

METHODS: The Mayo Clinic medical record was interrogated for patients prescribed lorlatinib between July 2017 and May 2022, and medical records were reviewed in detail.

RESULTS: Sixty-three patients were prescribed lorlatinib (median age: 59 years (range: 37-82); 31 (49%) men). Twenty-five (40%) developed a neurocognitive adverse event, which had been characterized as follows: “hallucinations,” “noise confusion,” “obtunded,” “memory loss,” “trouble doing simple tasks,” “mental fogginess,” “vivid dreams,” and “nightmares.” In univariable analyses, age, gender, prior brain metastases, concomitant CYP3A inducers or inhibitors, and married/partner status were not statistically significantly predictive of the neurocognitive adverse event. In multivariable analyses, older age (≥ 65 years) was predictive (HR: 2.6 (95% CI: 1.09, 6.26); p = 0.03). Notably, 3 of 14 married/partnered patients (21%) and 5 of 6 non-married/partnered patients (83%) were hospitalized for a neurocognitive adverse event (p = 0.02, Fisher’s Exact test). Medical record content corroborated the importance of married/partnered (“spouse is very supportive”) and of non-married/partnered status (“patient lives alone” and “children some distance away”).

CONCLUSIONS: This study further characterized lorlatinib-associated neurocognitive adverse events and confirmed older age as a risk factor. Importantly, social support may prevent hospitalization for a neurocognitive adverse event, and, thus, merits further study, perhaps in older patients.

PMID:41291327 | DOI:10.1007/s00520-025-10182-9