Nevin Manimala

Bioinformatics. 2025 Jan 29:btaf034. doi: 10.1093/bioinformatics/btaf034. Online ahead of print.

ABSTRACT

MOTIVATION: The accurate prediction of O-GlcNAcylation sites is crucial for understanding disease mechanisms and developing effective treatments. Previous machine learning models primarily relied on primary or secondary protein structural and related properties, which have limitations in capturing the spatial interactions of neighboring amino acids. This study introduces local environmental features as a novel approach that incorporates three-dimensional spatial information, significantly improving model performance by considering the spatial context around the target site. Additionally, we utilize sparse recurrent neural networks to effectively capture sequential nature of the proteins and to identify key factors influencing O-GlcNAcylation as an explainable machine learning model.

RESULTS: Our findings demonstrate the effectiveness of our proposed features with the model achieving an F1 score of 28.3%, as well as feature selection capability with the model using only the top 20% of features achieving the highest F1 score of 32.02%, a 1.4-fold improvement over existing PTM models. Statistical analysis of the top 20 features confirmed their consistency with literature. This method not only boosts prediction accuracy but also paves the way for further research in understanding and targeting O-GlcNAcylation.

AVAILABILITY: The entire code, data, features used in this study are available in the GitHub repository: https://github.com/pseokyoung/o-glcnac-prediction.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:39878910 | DOI:10.1093/bioinformatics/btaf034

Eur Radiol. 2025 Jan 29. doi: 10.1007/s00330-025-11387-6. Online ahead of print.

ABSTRACT

OBJECTIVE: To conduct a meta-analysis assessing the diagnostic performance of the node reporting and data system (Node-RADS) for detecting lymph node (LN) invasion.

METHOD: We performed a systematic literature search of online scientific publication databases from inception up to July 31, 2024. We used the quality assessment of diagnostic accuracy studies-2 (QUADAS-2) to assess the study quality, and heterogeneity was determined by the Q-test and measured with I² statistics. We employed the hierarchic summary ROC (HSROC) model to estimate the summary sensitivity and specificity. Subgroup analyses were conducted according to the imaging modality and cutoff values.

RESULTS: A total of 13 studies involving 1341 participants met the inclusion criteria. Pooled summary estimates of sensitivity, specificity, and area under the curve of HSROC were 0.79 (95% CI: 0.66-0.88), 0.86 (95% CI: 0.80-0.90), and 0.90 (95% CI: 0.87-0.92). Subgroup analysis showed that the pooled sensitivity and specificity for CT were 0.74 (95% CI: 0.63-0.83) and 0.84 (95% CI: 0.74-0.91), whereas for MRI were 0.84 (95% CI: 0.59-0.95) and 0.88 (95% CI: 0.81-0.93), respectively.

CONCLUSION: Node-RADS demonstrates the promising potential for the prediction of LN invasion, with high specificity but moderate sensitivity, particularly with optimal cutoff value ≥ 3. Indirect comparisons showed no significant difference between CT and MRI regarding overall diagnostic accuracy.

KEY POINTS: Question Since the Node-RADS has been proposed, a number of studies have assessed its diagnostic performance for evaluating LN invasion. Findings Node-RADS demonstrated high specificity but moderate sensitivity, and cutoff ≥ 3 is the optimal threshold; indirect comparison suggested no significant difference between CT and MRI. Clinical relevance This study synthesized currently available evidence on studies of utilizing Node-RADS for assessing LNI in patients with various cancers, providing valuable insights for radiologists for utilizing this new risk scoring system in clinical practice.

PMID:39878903 | DOI:10.1007/s00330-025-11387-6

Eur Radiol. 2025 Jan 29. doi: 10.1007/s00330-025-11369-8. Online ahead of print.

ABSTRACT

OBJECTIVES: To analyze the CT imaging features of extranodal natural killer/T (NK/T)-cell lymphoma, nasal type (ENKTCL-NT) involving the gastrointestinal tract (GI), and to compare them with those of Crohn’s disease (CD) and diffuse large B-cell lymphoma (DLBCL).

MATERIALS AND METHODS: Data were retrospectively collected from 17 patients diagnosed with GI ENKTCL-NT, 68 patients with CD, and 47 patients with DLBCL. The CT findings of ENKTCL-NT were analyzed and compared with those of CD and DLBCL. Data were analyzed using SPSS (version 25.0) and MedCalc (version 18.2.1). p < 0.05 was considered statistically significant.

RESULTS: The 17 patients with ENKTCL-NT included 11 males (64.7%) and 6 females (35.3%) (mean age, 46.41 ± 4.12 years). The CT features of ENKTCL-NT included: circumferential symmetric thickening (100%), moderate thickening (70.6%), skip lesions (52.9%), contiguous lesion (47.1%), mucosal or layered enhancement (70.6%), moderate mural enhancement (64.7%) with non-enhanced regions (47.1%), absence of lymphadenopathy (76.5%), bowel perforation or fistula (17.6%), and peri-enteric blurred fat space (70.6%). The presence of circumferential symmetric thickening, moderate mural enhancement, and non-enhanced regions were more indicative of ENKTCL-NT than CD (17/17 vs. 17/68, 11/17 vs. 22/68, 8/17 vs. 0/68, p < 0.05). The presence of skip lesions, mucosal or layered enhancement, and absence of peri-enteric lymphadenopathy were more indicative of ENKTCL-NT than DLBCL (9/17 vs. 2/47, 12/17 vs. 1/37, 13/17 vs. 19/47, p < 0.05).

CONCLUSION: CT imaging features can provide useful information for the early diagnosis of ENKTCL-NT and effectively differentiate it from CD and DLBCL.

KEY POINTS: Question Extranodal natural killer/T-cell lymphoma, nasal type (ENKTCL-NT) involving the gastrointestinal tract (GI) is highly malignant but easily misdiagnosed by clinicians and endoscopic examination. Findings CT could provide useful information in the diagnosis of ENKTCL-NT involving GI and in differentiating it from Crohn’s disease and diffuse large B-cell lymphoma. Clinical relevance This study will help improve the ability of radiologists to diagnose ENKTCL-NT involving GI, and a more predictive diagnosis will also alert clinicians to perform multiple deep endoscopic biopsies, which will contribute to the early diagnosis and treatment of ENKTCL-NT.

PMID:39878902 | DOI:10.1007/s00330-025-11369-8

Eur J Nucl Med Mol Imaging. 2025 Jan 29. doi: 10.1007/s00259-024-07061-6. Online ahead of print.

ABSTRACT

PURPOSE: The positron range effect can impair PET image quality of Gallium-68 (⁶⁸Ga). A positron range correction (PRC) can be applied to reduce this effect. In this study, the effect of a tissue-independent PRC for ⁶⁸Ga was investigated on patient data.

METHODS: PET/CT data (40 patients: [⁶⁸Ga]Ga-DOTATOC or [⁶⁸Ga]Ga-PSMA) were reconstructed using Q.Clear reconstruction algorithm. Two reconstructions were performed per patient, Q.Clear with and without PRC. SUV_max and contrast-to-noise ratio (CNR) values per lesion were compared between PRC and non-PRC images. Five experienced nuclear medicine physicians reviewed the images and chose the preferred reconstruction based on the image quality, lesion detectability, and diagnostic confidence.

RESULTS: A total of 155 lesions were identified. The PRC resulted in statistically significant increase of the SUV_max and CNR for soft tissue lesions (6.4%, p < 0.001; 8.6%, p < 0.001), bone lesions (14.6%, p < 0.001; 12.5%, p < 0.001), and lung lesions (3.6%, p = 0.010; 6.3%, p = 0.001). This effect was most prominent in small lesions (SUV_max: 12.0%, p < 0.001, and CNR: 13.0%, p < 0.001). Similar or better image quality, lesion detectability, and diagnostic confidence was achieved in PRC images compared to the non-PRC images as those assessed by the expert readers.

CONCLUSIONS: A tissue-independent PRC increased the SUV_max and CNR in soft tissue, bone, and lung lesions with a larger effect for the small lesions. Visual assessment demonstrated similar or better image quality, lesion detectability, and diagnostic confidence in PRC images compared to the non-PRC images.

PMID:39878896 | DOI:10.1007/s00259-024-07061-6

Asian Pac Isl Nurs J. 2025 Jan 28;9:e56667. doi: 10.2196/56667.

ABSTRACT

BACKGROUND: Neuromuscular disorders (NMDs) constitute a heterogeneous group of disorders that affect motor neurons, neuromuscular junctions, and muscle fibers, resulting in symptoms such as muscle weakness, fatigue, and reduced mobility. These conditions significantly affect patients’ quality of life and impose a substantial burden on caregivers. Spinal muscular atrophy (SMA) is a relatively common NMD in children that presents in various types with varying degrees of severity.

OBJECTIVE: This study aimed to evaluate the sleep quality of children with NMDs, particularly SMA types 1, 2, and 3 and assess the stress levels experienced by their parents.

METHODS: A descriptive analytical study was conducted from February to October 2023, in selected hospitals and dystrophy associations in Tehran and Isfahan, Iran. A total of 207 children aged 1-14 years with various NMDs were included in the study. Data were collected using a web-based questionnaire with 3 parts: demographic information, the Children’s Sleep Habits Questionnaire to assess children’s sleep, and the Stress Response Inventory to measure parental stress. Statistical analyses were performed using SPSS version 22, with an α level of .05.

RESULTS: Significant differences in sleep quality were found among SMA types, with mean scores of 74.76 (SD 7.48) for SMA type 1, 76.4 (SD 7.29) for SMA type 2, 72.88 (SD 6.73) for SMA type 3, and 75.87 (SD 5.74) for other NMDs (P=.02). A correlation was found between sleep and length of hospital stay (r=0.234, P<.001)and between sleep and the child’s sex (r=-0.140, P=.04). Parental stress scores averaged 95.73 (SD 32.12). There was not a statistically significant difference in parental stress scores among the 4 groups (P=.78). This suggests that parental stress levels were similar across different NMD groups.

CONCLUSIONS: Sleep disorders are prevalent among children with NMDs, especially SMA. Parents experience high levels of stress that can affect the care they provide. Therefore, interventions to improve children’s sleep and address parental stress are crucial. Regular screening, counseling, and tailored support are recommended to enhance the well-being of children with NMDs and their families.

PMID:39878075 | DOI:10.2196/56667

Int J Surg. 2025 Jan 28. doi: 10.1097/JS9.0000000000002249. Online ahead of print.

ABSTRACT

BACKGROUND: While recent randomized controlled trials have demonstrated that sublobar resection is non-inferior to lobectomy, the comparative efficacy of these procedures remains uncertain for early-stage non-small cell lung cancer (NSCLC; ≤ 3 cm) exhibiting invasive features postoperatively, such as visceral pleural invasion (VPI) or spread through air spaces (STAS).

MATERIALS AND METHODS: To identify eligible studies, a comprehensive search of PubMed, Embase, MEDLINE, the Cochrane Library, and Web of Science was conducted through 25 July 2024. Studies were screened according to predefined criteria in accordance with PRISMA guidelines. The primary endpoints were 5-year overall survival (OS) and recurrence-free survival (RFS). Hazard ratios (HR) and 95% confidence intervals (CI) were used to perform a meta-analysis.

RESULTS: The final analysis included 14 retrospective studies and 1 randomized controlled trial, encompassing a total of 8,054 patients with NSCLC (tumors ≤3 cm) exhibiting VPI or STAS. The meta-analysis revealed that sublobar resection was associated with impaired 5-year OS (HR: 1.25; 95% CI: 1.10-1.41) and slightly inferior RFS (HR: 1.25; 95% CI: 0.99-1.58) compared to lobectomy for pT2a (VPI) NSCLC patients with tumor ≤3 cm. Similarly, sublobar resection was associated with significantly worse 5-year OS (HR: 2.58; 95% CI: 1.92-3.45) and 5-year RFS (HR: 2.42; 95% CI: 1.69-3.46) compared to lobectomy for stage IA NSCLC patients with STAS. Subgroup analysis revealed that statistically significant differences in 5-year OS (HR: 1.13; 95% CI: 0.92-1.38) and 5-year RFS (HR: 0.87; 95% CI: 0.56-1.36) were not observed between the sublobar resection and lobectomy groups for pT2a (VPI) NSCLC patients with tumor ≤2 cm. Additionally, no statistically significant survival difference was observed between the segmentectomy and lobectomy groups for NSCLC patients (≤3 cm) with VPI (5-year OS: HR: 1.16; 95% CI: 0.89-1.52; 5-year RFS: HR: 1.07; 95% CI: 0.88-1.30) or STAS (5-year OS: HR: 3.88; 95% CI: 0.82-18.31; 5-year RFS: HR: 1.64; 95% CI: 0.70-3.80).

CONCLUSION: For early-stage (≤3 cm) NSCLC with VPI or STAS, sublobar resection was associated with worse survival outcomes compared to lobectomy. However, segmentectomy achieved survival outcomes comparable to those of lobectomy. For pT2a (VPI) NSCLC patients with tumor ≤2 cm, the differences in survival outcomes between sublobar resection and lobectomy were not statistically significant.

PMID:39878072 | DOI:10.1097/JS9.0000000000002249

J Clin Ultrasound. 2025 Jan 29. doi: 10.1002/jcu.23922. Online ahead of print.

ABSTRACT

BACKGROUND: To investigate the performance of contrast-enhanced ultrasound(CEUS) parameters of metastatic axillary lymph nodes (ALNs) before and after two courses of neoadjuvant chemotherapy (NAC) in breast cancer patients in predicting the efficacy of NAC.

METHODS: A total of 41 postoperative breast cancer patients were selected. All patients underwent NAC, and ALN biopsy was positive before chemotherapy. Metastatic ALN was examined by CEUS before and after two courses of NAC. The CEUS parameters of metastatic ALNs before and after two courses of NAC were analyzed to determine the performance of CEUS parameters in predicting the efficacy of NAC in early stage.

RESULTS: The NAC was effective for 28 cases and ineffective for 13 cases. There were no statistically significant differences in the CEUS parameters between effective NAC and ineffective NAC individuals before and after two courses of NAC. But, there were statistically significant differences in long diameter (LD), short diameter (SD), Peak intensity (Peak%) and area under the curve (AUC) between the effective and ineffective NAC patients after two courses of NAC. Receiver operating characteristic curve (ROC) analysis suggested the drop-out value of LD, SD, Peak% and AUC after two courses of NAC can be used as important indicators to evaluate the efficacy of NAC (p < 0.05).

CONCLUSIONS: CEUS parameters of metastatic axillary lymph nodes (ALNs) before and after two courses of neoadjuvant chemotherapy (NAC) in breast cancer patients can predict the efficacy of NAC in early stage.

PMID:39878049 | DOI:10.1002/jcu.23922

Clin Infect Dis. 2025 Jan 29:ciae620. doi: 10.1093/cid/ciae620. Online ahead of print.

ABSTRACT

BACKGROUND: Cabotegravir + rilpivirine (CAB + RPV) administered via intramuscular gluteal injections is the first complete long-acting regimen for maintaining human immunodeficiency virus type 1 (HIV-1) virologic suppression. We present substudy results on short-term repeat intramuscular CAB + RPV long-acting thigh injections in participants with ≥3 years of experience with gluteal administration during the ATLAS-2M study.

METHODS: Substudy phases included screening, thigh injection (day 1-week 16), and return to gluteal injection (week 16-week 24). The injection schedule was unchanged from the main study. Outcomes included pharmacokinetics, safety, tolerability, efficacy, and patient-reported outcomes. Pharmacokinetic parameters were determined using noncompartmental analysis and mixed-effects modeling. Population pharmacokinetic simulations were performed.

RESULTS: There were 118 participants. In the arm that received injections every 2 months (Q2M), first CAB thigh injection including area under the concentration-time curve and maximum observed concentration (Cmax) and first RPV thigh injection Cmax and all last RPV thigh injection parameters were statistically higher vs gluteal injections (paired comparison). No significant differences occurred with once-monthly (QM) dosing. No participants had HIV-1 RNA ≥50 copies/mL after thigh injections. Overall, 4%-7% of injection site reactions (ISRs) were grade 3. Five participants withdrew due to an ISR or injection intolerability. Overall, 30% preferred thigh vs gluteal injections. Simulations demonstrated the potential for chronic/continuous QM or ≤2 consecutive Q2M thigh injections.

CONCLUSIONS: These data demonstrate the potential use of chronic/continuous QM and rotational/short-term QM or Q2M (≤4 months of continuous dosing), CAB + RPV long-acting intramuscular thigh administration for HIV-1 treatment.

PMID:39878031 | DOI:10.1093/cid/ciae620

Swiss Med Wkly. 2025 Jan 2;155:3669. doi: 10.57187/s.3669.

ABSTRACT

AIMS: We aimed to explore atrial fibrillation (AF)-induced productivity losses in working-age atrial fibrillation patients and to estimate atrial fibrillation-related indirect costs.

METHODS: Between 2014 and 2017, the Swiss Atrial Fibrillation prospective cohort study (Swiss-AF) enrolled 217 working-age patients with documented atrial fibrillation. Self-reported changes in professional activity and the reasons thereof were descriptively analysed over 8 years of follow-up or until patients reached the retirement age. Results were put into perspective, and indirect costs were planned to be estimated, through comparison with a general population-based, age-, sex- and year-matched comparison sample from the Swiss labour force survey (SLFS).

RESULTS: Of 217 analysed Swiss-AF patients, 14.7% reported a professional activity change (9.2% stop, 5.5% reduction) due to atrial fibrillation before the end of observation. Of those working at enrolment (n = 157), 3.8% had a subsequent professional activity change due to atrial fibrillation, 11.6% due to other reasons. Patients were more likely to report an impact of atrial fibrillation on professional activity if they had had atrial fibrillation longer and were closer to the retirement age. Slightly fewer Swiss-AF patients were employed (75%) than in the comparison sample (77%). For those working however, the degree of employment was higher (88% vs 83%). Lack of differences between the Swiss-AF patients and the comparison sample indicated no relevant indirect costs of atrial fibrillation due to lost productivity.

CONCLUSION: Only a minority of atrial fibrillation patients reported a negative impact of atrial fibrillation on their professional activity. Professional activity changes due to other reasons were reported more frequently. Compared with the general population, atrial fibrillation did not cause distinct differences.

PMID:39878030 | DOI:10.57187/s.3669

Nanoscale. 2025 Jan 29. doi: 10.1039/d4nr04879b. Online ahead of print.

ABSTRACT

Mixing different metal ions at the B site of ABX₃ perovskites offers a promising approach for addressing challenges related to toxicity, stability and performance in optoelectronic applications. One such example is CsPb_1-xSn_xBr₃ which addresses the toxicity issue posed by lead while allowing us to tune optoelectronic properties such as the band gap. In this work, nearly monodisperse CsPb_1-xSn_xBr₃ quantum dots (QDs) were synthesized with variable Pb/Sn compositions, i.e. CsPbBr₃, CsPb_0.9Sn_0.1Br₃ and CsPb_0.7Sn_0.3Br₃. The photoluminescence quantum yield (PLQY) of CsPb_1-xSn_xBr₃ first increases for x = 0.1 and then decreases for x = 0.3 with respect to x = 0. Such an effect of Sn incorporation on the PLQY was investigated using photoblinking studies which revealed three levels of blinking statistics namely ON, GRAY and OFF. These results along with the excited state lifetime measurements enabled us to understand charge carrier dynamics in the CsPb_1-xSn_xBr₃ QDs. Based on our findings, we propose that the photogenerated hot electrons of Sn enhance the PLQY by filling the trap states centered on Pb, which otherwise promote non-radiative relaxations in the Sn-free CsPbBr₃. However, at higher Sn concentrations, non-radiative recombination becomes more pronounced, reducing the PLQY.

PMID:39878025 | DOI:10.1039/d4nr04879b