Tag: nevin manimala

Bioinformatics. 2024 Jun 18:btae374. doi: 10.1093/bioinformatics/btae374. Online ahead of print.

ABSTRACT

MOTIVATION: Single-cell omics technologies have enabled the quantification of molecular profiles in individual cells at an unparalleled resolution. Deep learning, a rapidly evolving sub-field of machine learning, has instilled a significant interest in single-cell omics research due to its remarkable success in analysing heterogeneous high-dimensional single-cell omics data. Nevertheless, the inherent multi-layer nonlinear architecture of deep learning models often makes them ‘black boxes’ as the reasoning behind predictions is often unknown and not transparent to the user. This has stimulated an increasing body of research for addressing the lack of interpretability in deep learning models, especially in single-cell omics data analyses, where the identification and understanding of molecular regulators are crucial for interpreting model predictions and directing downstream experimental validations.

RESULTS: In this work, we introduce the basics of single-cell omics technologies and the concept of interpretable deep learning. This is followed by a review of the recent interpretable deep learning models applied to various single-cell omics research. Lastly, we highlight the current limitations and discuss potential future directions.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:38889275 | DOI:10.1093/bioinformatics/btae374

Bioinformatics. 2024 Jun 18:btae375. doi: 10.1093/bioinformatics/btae375. Online ahead of print.

ABSTRACT

MOTIVATION: Nanopore direct RNA sequencing (DRS) enables the detection of RNA N6-methyladenosine (m6A) without extra laboratory technique. A number of supervised or comparative approaches have been developed to identify m6A from Nanopore DRS reads. However, existing methods typically utilize either statistical features of the current signals or basecalling error features, ignoring the richer information of the raw signals of DRS reads.

RESULTS: Here, we propose RedNano, a deep-learning method designed to detect m6A from Nanopore DRS reads by utilizing both raw signals and basecalling errors. RedNano processes the raw-signal feature and basecalling-error feature through residual networks. We validated the effectiveness of RedNano using synthesized, Arabidopsis, and human DRS data. The results demonstrate that RedNano surpasses existing methods by achieving higher AUCs and AUPRs in all three datasets. Furthermore, RedNano performs better in cross-species validation, demonstrating its robustness. Additionally, when detecting m6A from an independent dataset of P. trichocarpa, RedNano achieves the highest AUC and AUPR, which are 3.8-9.9% and 5.5-13.8% higher than other methods, respectively.

AVAILABILITY AND IMPLEMENTATION: The source code of RedNano is freely available at https://github.com/Derryxu/RedNano.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:38889266 | DOI:10.1093/bioinformatics/btae375

Circ Cardiovasc Interv. 2024 Jun;17(6):e013466. doi: 10.1161/CIRCINTERVENTIONS.123.013466. Epub 2024 Jun 18.

ABSTRACT

BACKGROUND: Procedure volumes are associated with outcomes for many cardiovascular procedures, leading to guidelines on minimum volume thresholds for certain procedures; however, the volume-outcome relationship with left atrial appendage occlusion is poorly understood. As such, we sought to determine the relationship between hospital and physician volume and WATCHMAN left atrial appendage occlusion procedural success overall and with the new generation WATCHMAN FLX device.

METHODS: We performed an analysis of WATCHMAN procedures (January 2019 to October 2021) from the National Cardiovascular Data Registry LAAO Registry. Three-level hierarchical generalized linear models were used to assess the adjusted relationship between procedure volume and procedural success (device released with peridevice leak <5 mm, no in-hospital major adverse events).

RESULTS: Among 87 480 patients (76.2±8.0 years; 58.8% men; mean CHA₂DS₂-VASc score, 4.8±1.5) from 693 hospitals, the procedural success rate was 94.2%. With hospital volume Q4 (greatest volume) as the reference, the likelihood of procedural success was significantly less among Q1 (odds ratio [OR], 0.66 [CI, 0.57-0.77]) and Q2 (OR, 0.78 [CI, 0.69-0.90]) but not Q3 (OR, 0.95 [CI, 0.84-1.07]). With physician volume Q4 (greatest volume) as the reference, the likelihood of procedural success was significantly less among Q1 (OR, 0.72 [CI, 0.63-0.82]), Q2 (OR, 0.79 [CI, 0.71-0.89]), and Q3 (OR, 0.88 [CI, 0.79-0.97]). Among WATCHMAN FLX procedures, there was attenuation of the volume-outcome relationships, with statistically significant but modest absolute differences of only ≈1% across volume quartiles.

CONCLUSIONS: In this contemporary national analysis, greater hospital and physician WATCHMAN volumes were associated with increased procedure success. The WATCHMAN FLX transition was associated with increased procedural success and less heterogeneity in outcomes across volume quartiles. These findings indicate the importance of understanding the volume-outcome relationship for individual left atrial appendage occlusion devices.

PMID:38889251 | DOI:10.1161/CIRCINTERVENTIONS.123.013466

JBJS Rev. 2024 Jun 18;12(6). doi: 10.2106/JBJS.RVW.24.00067. eCollection 2024 Jun 1.

ABSTRACT

BACKGROUND: Multiple hemiarthroplasty (HA) approaches exist for femoral neck fracture (FNF) treatment. However, there is no consensus on the superiority of one approach for postoperative outcomes. This study assessed outcomes among randomized controlled trials (RCTs) comparing the posterior approach (PA), direct lateral approach (DLA), anterolateral approach (ALA), and the direct anterior approach (DAA) in HA for FNF.

METHODS: PubMed, Ovid/MEDLINE, Scopus, Cochrane Central Registry of Controlled Trials, and Cochrane Database of Systematic Reviews were queried in February 2024. A frequentist model network meta-analysis of eligible prospective RCTs compared outcomes among approaches using P-scores.

RESULTS: Of 1,481 retrieved studies, 11 RCTs totaling 1,513 FNF patients who underwent HA through a PA (n = 446; 29.5%), DLA (n = 481; 31.8%), ALA (n = 296; 19.6%), or DAA (n = 290; 19.2%) with median (interquartile range) follow-up of 6 (4.5-12.0) months were included for meta-analysis. DAA was associated with statistically increased operative duration (mean difference [MD], 1.89 minutes; 95% CI, 0.08 to 3.69 minutes; p < 0.001) compared with a PA, whereas an ALA was associated with statistically greater blood loss compared with a PA (MD, 5.81 mL; 95% CI, 4.11 to 7.50 mL; p < 0.001). There were no differences in the incidence of fracture, dislocation, infection, complications, revision, nor 1-year mortality among approaches. There were also no differences in hip nor pain score improvement at latest follow-up, although with high heterogeneity (I2 = 85.7% and 94.2%, respectively).

CONCLUSION: This study found no clinical difference in improvement in pain, function, nor in revision outcomes and operative characteristics among HA approaches for FNF, and each approach had a similar adverse event profile. Despite limited randomized evidence, these findings suggest comparable short-term efficacy and safety of all approaches.

LEVEL OF EVIDENCE: Therapeutic, Level I. See Instructions for Authors for a complete description of levels of evidence.

PMID:38889234 | DOI:10.2106/JBJS.RVW.24.00067

Med Care. 2024 Jun 11. doi: 10.1097/MLR.0000000000002023. Online ahead of print.

ABSTRACT

OBJECTIVE: The Medicare Annual Wellness Visit (AWV)-a prevention-focused annual check-up-has been available to beneficiaries with Part B coverage since 2011. The objective of this study was to estimate the effect of Medicare AWVs on breast cancer screening and diagnosis.

DATA SOURCES AND STUDY SETTING: The National Cancer Institute’s Surveillance, Epidemiology, and End Results cancer registry data linked to Medicare claims (SEER-Medicare), HRSA’s Area Health Resources Files, the FDA’s Mammography Facilities database, and CMS “Mapping Medicare Disparities” utilization data from 2013 to 2015.

STUDY DESIGN: Using an instrumental variables approach, we estimated the effect of AWV utilization on breast cancer screening and diagnosis, using county Welcome to Medicare Visit (WMV) rates as the instrument.

DATA COLLECTION/EXTRACTION METHODS: 66,088 person-year observations from 49,769 unique female beneficiaries.

PRINCIPAL FINDINGS: For every 1-percentage point increase in county WMV rate, the probability of AWV increased by 1.7 percentage points. Having an AWV was associated with a 22.4-percentage point increase in the probability of receiving a screening mammogram within 6 months (P<0.001). There was no statistically significant increase in the probability of breast cancer diagnosis (overall or early stage) within 6 months of an AWV. Findings were robust to multiple model specifications.

CONCLUSIONS: Performing routine cancer screening is an evidence-based practice for diagnosing earlier-stage, more treatable cancers. The Medicare Annual Wellness Visit effectively increases breast cancer screening and may lead to more timely screening. Continued investment in Annual Wellness Visits supports breast cancer screening completion by women who are most likely to benefit, thus reducing the risk of overscreening and overdiagnosis.

PMID:38889206 | DOI:10.1097/MLR.0000000000002023

Scand J Urol. 2024 Jun 18;59:121-125. doi: 10.2340/sju.v59.40070.

ABSTRACT

PROBLEM: The aim of this study was to evaluate the change in LUTS in patients treated with RALP and to assess factors that may predict an improvement of LUTS.

MATERIALS AND METHOD: In our institutional prospective research registry, 1935 patients operated in the period between 2009 and 2021 with complete baseline- and 12-month EPIC-26 questionnaire were eligible for the study. Also SF-12 data estimating general quality of life (QoL) were analyzed. A LUTS summary score was constructed from the two questions concerning voiding stream/residual and frequency, and transformed linearly to a 0-100 scale with higher scores representing less symptoms A change of 6 points or more were considered Meaningful Clinical Differences (MCD). Two summary scores were calculated from the SF-12 – a mental component score (MCS-12) and a physical component score (PCS-12). Multivariate regression was used to estimate covariates associated with postoperative MCD, MCS-12 and PCS-12.

RESULTS: Mean change of LUTS-score showed an increase of 10 points 12-months post-RALP. 52% of patients achieved MCD. In multivariate logistic regression, preoperative LUTS was statistically significant associated with MCD. Reduction of LUTS was associated improved mean score of MCS-12 and PCS-12.

DISCUSSION AND CONCLUSION: Along with information about risk for urinary incontinence after RALP, patients with LUTS at baseline must be informed that these symptoms may be reduced after RALP. In our study, this LUTS reduction was associated with better general QoL.

PMID:38888041 | DOI:10.2340/sju.v59.40070

J Oral Rehabil. 2024 Jun 18. doi: 10.1111/joor.13784. Online ahead of print.

ABSTRACT

BACKGROUND: It can be challenging to perform activities of daily living in patients with chronic neck pain. As the severity of the pain increases, the quality of the movements decreases. Not only the neck, but also the shoulder, elbow, grip strength and psychomotor skills are affected by these pains.

OBJECTIVE: In this study, it was aimed to investigate the effect of neck pain on grip strength and psychomotor skills in adults diagnosed with chronic neck pain.

METHODS: A cross-sectional study was conducted to examine the effect of pain on grip strength and psychomotor skills in patients with chronic neck pain. This study was planned to be carried out between October 2019 and May 2020 at the Private Yaşam Medical Center in Adana, with the official permission of the institution manager, but this period was carried out between October 2019 and November 2020 due to the fact that sufficient number of patients could not be reached due to the COVID-19 global epidemic. A total of 80 individuals, including 40 control and 40 patients, were included in the study. Forty adult patients who applied to the clinic with a diagnosis of chronic neck pain and 40 healthy adults without a diagnosis of chronic neck pain were included in the study. Conducted with 80 adults between the age of 19 and 74 years old. Individuals were divided into Group 1-control group (n = 40) and Group 2-patient group (n&amp;#x02009;=&amp;#x02009;40). Information such as age, height, body weight and occupation of the groups were noted. Visual analogue scale and Neck Disability Index were applied to both the groups; hand grip strength with a Jamar hydraulic hand dynamometer, finger lateral grip strength with a pinchmeter and psychomotor skills with the Purdue Pegboard test were evaluated.

RESULTS: In the study, hand grip strength (p < .05), finger lateral grip strength (p < .05), psychomotor skills (p < .01) showed a statistically significant decrease in the patient group compared to the control group.

CONCLUSION: It is thought that in addition to the routine treatments for neck pain in the treatment plan of patients with chronic neck pain, exercises to improve the functionality and psychomotor skills in daily living activities can be included in the direction of increasing the grip strength and will guide future studies.

PMID:38888037 | DOI:10.1111/joor.13784

Int J Stroke. 2024 Jun 18:17474930241264686. doi: 10.1177/17474930241264686. Online ahead of print.

ABSTRACT

BACKGROUND: Stroke prevention is a pressing global health priority, with reducing elevated lipids recognized as a key strategy. East Asians, constituting over 1.6 billion individuals and the largest racial group worldwide, are a key demographic in this effort. Yet, the effectiveness of lipid-lowering therapies for stroke prevention in this population remains uncertain.

AIMS AND METHODS: We conducted a systematic review and meta-analysis of large-scale randomized controlled trials (RCTs) with at least 3 years of follow-up to evaluate the long-term impact of lipid-lowering therapies on stroke incidence in East Asians. We systematically searched four electronic databases up to January 11, 2024. The association was quantified using relative risk (RR) with a 95% confidence interval (CI), and between-study heterogeneity was evaluated using the I2 statistic. Additionally, we utilized the Cochrane Risk of Bias Tool to assess the risk of bias in each included RCT and applied the GRADE approach to evaluate the certainty of the evidence.

RESULTS: This study incorporated data from 9 large-scale RCTs involving 54,354 participants. Our findings of overall analyses revealed that lipid-lowering therapies did not significantly affect the long-term incidence of all strokes (9 RCTs; 54,354 participants; RR, 0.98 [95% CI, 0.87-1.10]; P = 0.75), ischemic stroke (7 RCTs; 52,059 participants; RR, 0.91 [95% CI, 0.79-1.04]; P = 0.16), or hemorrhage stroke (7 RCTs; 52,059 participants; RR, 1.24 [95% CI, 0.97-1.59]; P = 0.09) in East Asians. Notably, there was no evidence of heterogeneity or publication bias, and the quality of evidence assessed using GRADE methodologies was rated as high. Sensitivity analyses confirmed the robustness of our results, with no single study significantly affecting the overall findings. Furthermore, subgroup analyses consistently supported the conclusions, further bolstering the reliability of our study.

CONCLUSIONS: Lipid-lowering therapies did not demonstrate any beneficial effects on long-term stroke prevention among East Asians.

PMID:38888036 | DOI:10.1177/17474930241264686

Oral Dis. 2024 Jun 18. doi: 10.1111/odi.15042. Online ahead of print.

ABSTRACT

OBJECTIVE: To analyze trends of antibiotic consumption and expenditure in Chinese stomatology hospitals between 2014 and 2018 with a longitudinal study design, and show the impacts of the comprehensive policy on dental antibiotic use in China.

SUBJECT AND METHODS: Consumption was quantified as the number of daily defined doses (DDDs) and expenditure as the procurement costs, using medical institutions’ drug procurement data from the Chinese Monitoring Network for Rational Use of Drugs. Descriptive statistics was employed and the compound annual growth rate (CAGR) was calculated to show the average annual growth rate.

RESULTS: Between 2014 and 2018, overall antibiotic consumption increased from 842.6 thousand DDDs to 1376.7 thousand DDDs (p < 0.001) and expenditure increased from 11.6 million RMB to 20.9 million RMB (p < 0.001), where other β-lactam antibacterials accounted for the largest proportion of total consumption (37.1%-50.1%) and expenditure (52.9%-66.6%), and also increase the largest (CAGR = 18.4%, p < 0.001). The proportion of oral antibiotics was nearly 9 times of parenteral antibiotics in consumption (CAGR = 0.3%, p = 0.023) and only 2 times in expenditure (CAGR = -1.7%, p = 0.112). The non-restricted group accounted for more than 90% of consumption (CAGR = 0.6%, p < 0.001). In 2018, oral first-generation cephalosporins (22.8%), oral imidazole derivatives (22.3%), and oral second-generation cephalosporins (19.2%) were the most frequently used antibiotic classification, while parenteral second-generation cephalosporins were top one (19.8%) for expenditure. At chemical substance levels, the consumption of oral cefradine ranked top one (21.4%) and parenteral cefuroxime accounted for the largest proportion of expenditure (14.5%) in 2018. Oral cefradine, oral metronidazole, and oral cefaclor were the top three frequently consumed antibiotics throughout the five years.

CONCLUSIONS: Despite the potential antibiotic overuse, the comprehensive antibiotic stewardship regulations of China got a satisfactory and better performance in dental practices. More effort is needed to establish more explicit guidelines to improve antibiotic stewardship, such as priority recommending amoxicillin and its derivatives for endodontic infections.

PMID:38888035 | DOI:10.1111/odi.15042

Khirurgiia (Mosk). 2024;(6):28-35. doi: 10.17116/hirurgia202406128.

ABSTRACT

OBJECTIVE: To demonstrate clinical features and outcomes in patients with cavitary lung lesions and COVID-19 associated pneumonia.

MATERIAL AND METHODS: A retrospective analysis of electronic medical records of 8261 patients with COVID-19 was performed. We selected 40 patients meeting the inclusion criteria. Sex, age, hospital-stay, lung tissue lesion, comorbidities, treatment, methods of respiratory support, complications and outcomes were evaluated.

RESULTS: Cavitary lung lesions were more common in men (67.5%). Age of patients ranged from 28 to 88 (mean 64.9±13.7) years. Hospital-stay in patients with cavitary lung lesions was 9-58 (median 27.5) days. There were 18 complications in 14 (35%) patients. Pneumothorax, isolated pneumomediastinum, pleural empyema, hemoptysis and sigmoid colon perforation were considered as complications of cavitary lung lesions. Nine (22.5%) patients died (5 of them with complications). Three patients died after surgical treatment. Long-term results were analyzed in 8 (25.8%) patients. Patients were followed-up for 3 months after discharge. Shrinkage of lesions occurred after 7-60 (mean 23) days, and complete obliteration of cavities came after 32 (range 14-90) days.

CONCLUSION: Cavitary lung lesions are a rare complication of COVID-19 pneumonia. There was no significant correlation of complications with age, sex, therapy, volume of lung lesions and non-invasive ventilation (NIV). Despite more common fatal outcomes in older patients undergoing NIV, the last one was prescribed exclusively due to disease progression and respiratory failure. Further research on this problem is necessary to identify possible risk factors of cavitary lung lesions.

PMID:38888016 | DOI:10.17116/hirurgia202406128