Nevin Manimala

J Proteome Res. 2024 Apr 30. doi: 10.1021/acs.jproteome.3c00902. Online ahead of print.

ABSTRACT

Traditional database search methods for the analysis of bottom-up proteomics tandem mass spectrometry (MS/MS) data are limited in their ability to detect peptides with post-translational modifications (PTMs). Recently, “open modification” database search strategies, in which the requirement that the mass of the database peptide closely matches the observed precursor mass is relaxed, have become popular as ways to find a wider variety of types of PTMs. Indeed, in one study, Kong et al. reported that the open modification search tool MSFragger can achieve higher statistical power to detect peptides than a traditional “narrow window” database search. We investigated this claim empirically and, in the process, uncovered a potential general problem with false discovery rate (FDR) control in the machine learning postprocessors Percolator and PeptideProphet. This problem might have contributed to Kong et al.‘s report that their empirical results suggest that false discovery (FDR) control in the narrow window setting might generally be compromised. Indeed, reanalyzing the same data while using a more standard form of target-decoy competition-based FDR control, we found that, after accounting for chimeric spectra as well as for the inherent difference in the number of candidates in open and narrow searches, the data does not provide sufficient evidence that FDR control in proteomics MS/MS database search is inherently problematic.

PMID:38687997 | DOI:10.1021/acs.jproteome.3c00902

JMIR Public Health Surveill. 2024 Apr 30;10:e54769. doi: 10.2196/54769.

ABSTRACT

BACKGROUND: The unprecedented emergence of the COVID-19 pandemic necessitated the development and global distribution of vaccines, making the understanding of global vaccine acceptance and hesitancy crucial to overcoming barriers to vaccination and achieving widespread immunization.

OBJECTIVE: This umbrella review synthesizes findings from systematic reviews and meta-analyses to provide insights into global perceptions on COVID-19 vaccine acceptance and hesitancy across diverse populations and regions.

METHODS: We conducted a literature search across major databases to identify systematic reviews and meta-analysis that reported COVID-19 vaccine acceptance and hesitancy. The AMSTAR-2 (A Measurement Tool to Assess Systematic Reviews) criteria were used to assess the methodological quality of included systematic reviews. Meta-analysis was performed using STATA 17 with a random effect model. The data synthesis is presented in a table format and via a narrative.

RESULTS: Our inclusion criteria were met by 78 meta-analyses published between 2021 and 2023. Our analysis revealed a moderate vaccine acceptance rate of 63% (95% CI 0.60%-0.67%) in the general population, with significant heterogeneity (I² = 97.59%). Higher acceptance rates were observed among health care workers and individuals with chronic diseases, at 64% (95% CI 0.57%-0.71%) and 69% (95% CI 0.61%-0.76%), respectively. However, lower acceptance was noted among pregnant women, at 48% (95% CI 0.42%-0.53%), and parents consenting for their children, at 61.29% (95% CI 0.56%-0.67%). The pooled vaccine hesitancy rate was 32% (95% CI 0.25%-0.39%) in the general population. The quality assessment revealed 19 high-quality, 38 moderate-quality, 15 low-quality, and 6 critically low-quality meta-analyses.

CONCLUSIONS: This review revealed the presence of vaccine hesitancy globally, emphasizing the necessity for population-specific, culturally sensitive interventions and clear, credible information dissemination to foster vaccine acceptance. The observed disparities accentuate the need for continuous research to understand evolving vaccine perceptions and to address the unique concerns and needs of diverse populations, thereby aiding in the formulation of effective and inclusive vaccination strategies.

TRIAL REGISTRATION: PROSPERO CRD42023468363; https://tinyurl.com/2p9kv9cr.

PMID:38687992 | DOI:10.2196/54769

JMIR Form Res. 2024 Apr 30;8:e54120. doi: 10.2196/54120.

ABSTRACT

BACKGROUND: Digital health technologies offer the potential to improve the daily lives of older adults, maintain their health efficiently, and allow aging in place. Despite increasing evidence of benefits and advantages, readiness for adopting digital interventions among older people remains underexplored.

OBJECTIVE: This study aims to explore the relationships between sociodemographic-, health-, and lifestyle-related factors and technology use in everyday life and community-dwelling older adults’ readiness to adopt telemedicine, smartphones with texting apps, wearables, and robotics.

METHODS: This was a cross-sectional, population-based survey study with a stratified probabilistic sample of adults aged 75 years or older living in South Tyrol (autonomous province of Bolzano/Bozen, Italy). A random sample of 3600 community-dwelling older adults living at home was invited to complete a questionnaire including single items (older adults’ readiness to use health technology) and scales (PRISMA-7; Program of Research on Integration of Services for the Maintenance of Autonomy). Descriptive and logistic regression analyses were performed to analyze the data.

RESULTS: In total, 1695 community-dwelling older adults completed the survey (for a response rate of 47%). In terms of potential digital health technology adoption, wearable devices were favored by 33.7% (n=571), telemedicine by 30.1% (n=510), smartphones and texting apps by 24.5% (n=416), and assistant robots by 13.7% (n=232). Sociodemographic-, health- and lifestyle-related factors, as well as the use of technology in everyday life, played a significant role in explaining readiness to adopt digital health technologies. For telemedicine, age ≥85 years (odds ratio [OR] 0.74, 95% CI 0.56-0.96), financial constraints (OR 0.68, 95% CI 0.49-0.95), and less than 2 hours of physical activity per week (OR 0.75, 95% CI 0.58-0.98) were associated with nonreadiness, while Italian-speaking participants (OR 1.54, 95% CI 1.16-2.05) and those regularly using computers (OR 1.74, 95% CI 1.16-2.60), smartphones (OR 1.69, 95% CI 1.22-2.35), and the internet (OR 2.26, 95% CI 1.47-3.49) reported readiness for adoption.

CONCLUSIONS: Community-dwelling older adults display varied readiness toward the adoption of digital health technologies, influenced by age, mother tongue, living situation, financial resources, physical activity, and current use of technology. The findings underscore the need for tailored interventions and educational programs to boost digital health technology adoption among community-dwelling older adults.

PMID:38687989 | DOI:10.2196/54120

Orbit. 2024 Apr 30:1-10. doi: 10.1080/01676830.2024.2343299. Online ahead of print.

ABSTRACT

PURPOSE: The posterior orbit is a confined space, harbouring neurovascular structures, frequently distorted by tumours. Image-guided navigation (IGN) has the potential to allow accurate localisation of these lesions and structures, reducing collateral damage whilst achieving surgical objectives.

METHODS: We assessed the feasibility, effectiveness and safety of using an electromagnetic IGN for posterior orbital tumour surgery via a comparative cohort study. Outcomes from cases performed with IGN were compared with a retrospective cohort of similar cases performed without IGN, presenting a descriptive and statistical comparative analysis.

RESULTS: Both groups were similar in mean age, gender and tumour characteristics. IGN set-up and registration were consistently achieved without significant workflow disruption. In the IGN group, fewer lateral orbitotomies (6.7% IGN, 46% non-IGN), and more transcutaneous lid and transconjunctival incisions (93% IGN, 53% non-IGN) were performed (p = .009). The surgical objective was achieved in 100% of IGN cases, with no need for revision surgery (vs 23% revision surgery in non-IGN, p = .005). There was no statistically significant difference in surgical complications.

CONCLUSION: The use of IGN was feasible and integrated into the orbital surgery workflow to achieve surgical objectives more consistently and allowed the use of minimal access approaches. Future multicentre comparative studies are needed to explore the potential of this technology further.

PMID:38687963 | DOI:10.1080/01676830.2024.2343299

J Cancer Res Ther. 2024 Apr 1;20(2):706-711. doi: 10.4103/jcrt.jcrt_498_23. Epub 2024 Apr 30.

ABSTRACT

BACKGROUND: Oral submucous fibrosis (OSF) is a precancerous lesion, with oral squamous cell carcinoma (OSCC) being the most prevalent malignancy affecting the oral mucosa. The malignant transformation of OSF into OSCC is estimated to occur in 7-13% of cases. Myofibroblasts (MFs) play pivotal roles in both physiological and pathological processes, such as wound healing and tumorigenesis, respectively. This study aimed to explore the involvement of MFs in the progression of OSF and its malignant transformation.

MATERIALS AND METHODS: In total, 94 formalin-fixed paraffin-embedded tissue blocks were collected, including normal oral mucosa (NOM; n = 10), early-moderate OSF (EMOSF; n = 29), advanced OSF (AOSF; n = 29), paracancerous OSF (POSF; n = 21), and OSCC (n = 5) samples. Alpha-smooth muscle actin was used for the immunohistochemical identification of MFs.

RESULTS: NOM exhibited infrequent expression of MFs. A higher staining index of MFs was found in AOSF, followed by EMOSF and NOM. Additionally, a significant increase in the staining index of MFs was found from EMOSF to POSF and OSCC. The staining index of MFs in NOM, EMOSF, AOSF, POSF, and OSCC was 0.14 ± 0.2, 1.69 ± 1.4, 2.47 ± 1.2, 3.57 ± 2.6, and 8.86 ± 1.4, respectively. All results were statistically significant (P < 0.05).

CONCLUSIONS: The expression of MFs exhibited a gradual increase as the disease progressed from mild to malignant transformation, indicating the contributory role of MFs in the fibrogenesis and potential tumorigenesis associated with OSF.

PMID:38687943 | DOI:10.4103/jcrt.jcrt_498_23

J Cancer Res Ther. 2024 Apr 1;20(2):651-657. doi: 10.4103/jcrt.jcrt_2017_23. Epub 2024 Apr 30.

ABSTRACT

BACKGROUND: The feasibility and safety of enhanced recovery after surgery (ERAS) for percutaneous computed tomography (CT)-guided microwave ablation (MWA) for treating lung nodules remain unclear.

METHODS AND MATERIALS: A total of 409 patients with lung tumors treated at the Department of Thoracic Surgery, First Affiliated Hospital of Guangxi Medical University from August 2020 to May 2023 were enrolled. Perioperative data, including baseline characteristics, operation time, postoperative pain score (visual analog scale [VAS]), hospitalization expenses, postoperative complications, total hospital stay, and patient satisfaction, were observed and recorded.

RESULTS: No perioperative mortality occurred in either group and complete ablation was achieved in all patients. Patients in the ERAS group had significantly shorter hospital stays (P < 0.001), reduced operation times (P = 0.047), lower hospitalization expenses (P < 0.001), lower VAS scores (P < 0.001), and fewer complications (P = 0.047) compared with the traditional group.

CONCLUSIONS: ERAS for percutaneous CT-guided MWA (ERAA) is safe, effective, and feasible for the treatment of lung nodules.

PMID:38687936 | DOI:10.4103/jcrt.jcrt_2017_23

J Cancer Res Ther. 2024 Apr 1;20(2):625-632. doi: 10.4103/jcrt.jcrt_1796_23. Epub 2024 Apr 30.

ABSTRACT

OBJECTIVE: To establish a multimodal model for distinguishing benign and malignant breast lesions.

MATERIALS AND METHODS: Clinical data, mammography, and MRI images (including T2WI, diffusion-weighted images (DWI), apparent diffusion coefficient (ADC), and DCE-MRI images) of 132 benign and breast cancer patients were analyzed retrospectively. The region of interest (ROI) in each image was marked and segmented using MATLAB software. The mammography, T2WI, DWI, ADC, and DCE-MRI models based on the ResNet34 network were trained. Using an integrated learning method, the five models were used as a basic model, and voting methods were used to construct a multimodal model. The dataset was divided into a training set and a prediction set. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the model were calculated. The diagnostic efficacy of each model was analyzed using a receiver operating characteristic curve (ROC) and an area under the curve (AUC). The diagnostic value was determined by the DeLong test with statistically significant differences set at P < 0.05.

RESULTS: We evaluated the ability of the model to classify benign and malignant tumors using the test set. The AUC values of the multimodal model, mammography model, T2WI model, DWI model, ADC model and DCE-MRI model were 0.943, 0.645, 0.595, 0.905, 0.900, and 0.865, respectively. The diagnostic ability of the multimodal model was significantly higher compared with that of the mammography and T2WI models. However, compared with the DWI, ADC, and DCE-MRI models, there was no significant difference in the diagnostic ability of these models.

CONCLUSION: Our deep learning model based on multimodal image training has practical value for the diagnosis of benign and malignant breast lesions.

PMID:38687933 | DOI:10.4103/jcrt.jcrt_1796_23

J Cancer Res Ther. 2024 Apr 1;20(2):592-598. doi: 10.4103/jcrt.jcrt_1627_23. Epub 2024 Apr 30.

ABSTRACT

OBJECTIVE: To analyze the characteristics of retracted oncology papers from Chinese scholars and the reasons for retraction.

METHODS: Data on retracted oncology papers from Chinese scholars published from 2013 to 2022 were retrieved from the Retraction Watch database. The retraction number and annual distribution, article types, reasons for retraction, retraction time delay, publishers, and journal characteristics of the retracted papers were analyzed.

RESULTS: A total of 2695 oncology papers from Chinese scholars published from 2013 to 2022 had been retracted. The majority of these papers were published from 2017 to 2020. In terms of article type, 2538 of the retracted papers were research articles, accounting for 94.17% of the total number of retracted papers. The main reasons for retraction were data, result, and image problems, duplicate publication, paper mills, author- and third-party-related reasons, plagiarism, false reviews, and method errors. The retraction time delay for the retracted papers ranged from 0 to 3582 days (median, 826 days). The retractions mainly occurred within the first 4 years after publication. A total of 77 publishers were involved in the retracted papers. In terms of journal distribution, 394 journals were involved in the retracted papers, of which 368 (93.40%) were included in the SCI database. There were 243 journals with an impact factor of <5 (66.03%).

CONCLUSION: In the field of oncology, the annual distribution of retracted papers from Chinese scholars exhibited first an increasing and subsequently a decreasing trend, reaching a peak in 2019, indicating an improvement in the status of retraction after 2021. The main type of the retracted papers was research article, and the main reason for retraction was academic misconduct. The retractions were mainly concentrated in several major publishers and periodicals in Europe and the United States. Most of the journals had low-impact factors.

PMID:38687929 | DOI:10.4103/jcrt.jcrt_1627_23

J Cancer Res Ther. 2024 Apr 1;20(2):555-562. doi: 10.4103/jcrt.jcrt_750_22. Epub 2023 Apr 5.

ABSTRACT

INTRODUCTION: There are emerging but inconsistent evidences about anti-epileptic drugs (AEDs) as radio- or chemo-sensitizers to improve survival in glioblastoma patients. We conducted a nationwide population-based study to evaluate the impact of concurrent AED during post-operative chemo-radiotherapy on outcome.

MATERIAL AND METHODS: A total of 1057 glioblastoma patients were identified by National Health Insurance Research Database and Cancer Registry in 2008-2015. Eligible criteria included those receiving surgery, adjuvant radiotherapy and temozolomide, and without other cancer diagnoses. Survival between patients taking concurrent AED for 14 days or more during chemo-radiotherapy (AED group) and those who did not (non-AED group) were compared, and subgroup analyses for those with valproic acid (VPA), levetiracetam (LEV), or phenytoin were performed. Multivariate analyses were used to adjust for confounding factors.

RESULTS: There were 642 patients in the AED group, whereas 415 in the non-AED group. The demographic data was balanced except trend of more patients in the AED group had previous drug history of AEDs (22.6% vs. 18%, P 0.078). Overall, the AED group had significantly increased risk of mortality (HR = 1.18, P 0.016) compared to the non-AED group. Besides, an adverse dose-dependent relationship on survival was also demonstrated in the AED group (HR = 1.118, P 0.0003). In subgroup analyses, the significant detrimental effect was demonstrated in VPA group (HR = 1.29,P 0.0002), but not in LEV (HR = 1.18, P 0.079) and phenytoin (HR = 0.98, P 0.862).

CONCLUSIONS: Improved survival was not observed in patients with concurrent AEDs during chemo-radiotherapy. Our real-world data did not support prophylactic use of AEDs for glioblastoma patients.

PMID:38687925 | DOI:10.4103/jcrt.jcrt_750_22

J Cancer Res Ther. 2024 Apr 1;20(2):547-554. doi: 10.4103/jcrt.jcrt_1246_23. Epub 2024 Apr 30.

ABSTRACT

OBJECTIVE: To investigate the safety and short- and long-term efficacy of ultrasound-guided microwave ablation (MWA) with parallel acupuncture for treating single hepatocellular carcinoma (HCC) in high-risk areas.

METHODS: Retrospective analysis was performed on 155 patients with single hepatocellular carcinoma who underwent microwave ablation in our hospital between December 2015 and September 2016. Patients with a tumor distance of ≤5 mm from the risk area were included in the observation group. Patients with a tumor distance of >5 mm from the risk area were placed in the control group. The patients’ preoperative general health status, tumor site, tumor size, follow-up data, disease-free survival rate, overall survival rates, local tumor progression, and intrahepatic distant recurrence rate were collected and analyzed.

RESULTS: The 1-, 3-, and 5-year overall survival rates for the observation group were 91.8%, 75.5%, and 59.2%, respectively. The 1-, 3-, and 5-year overall survival rates for the control group were 97.2%, 84.0%, and 66.0%, respectively. There were no significant differences between the two groups (P = 0.522). A tumor size of ≤20 mm (HR = 0.488, 95% CI = 0.254-0.940, P = 0.032) was an independent risk factor affecting the overall survival of patients with solitary HCC treated with MWA. The 1-, 3-, and 5-year recurrence-free survival rates for the observation group were 59.2%, 28.6%, and 18.4%, respectively, and those for the control group were 79.2%, 43.4%, and 31.1%, respectively. There was a statistical difference between the two groups (P = 0.007). Tumor size ≤20 mm (HR = 0.468, 95% CI = 0.303-0.723, P = 0.001), tumor location in a risk area (HR = 1.662, 95% CI = 1.121-2.465, P = 0.011), and an α-fetoprotein (AFP) level of <200 ug/L (HR = 0.612, 95% CI = 0.386-0.970, P = 0.036) are independent factors affecting the recurrence-free survival of MWA treatment for HCC.

CONCLUSION: Microwave ablation with parallel acupuncture guided by ultrasound is a safe and effective treatment for single hepatocellular carcinoma in high-risk areas.

PMID:38687924 | DOI:10.4103/jcrt.jcrt_1246_23