Category: Nevin Manimala

BMC Genom Data. 2023 May 2;24(1):26. doi: 10.1186/s12863-023-01128-3.

ABSTRACT

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

PMID:37131148 | DOI:10.1186/s12863-023-01128-3

BMC Med Educ. 2023 May 2;23(1):300. doi: 10.1186/s12909-023-04232-1.

ABSTRACT

INTRODUCTION: Formative assessment (FA) is an assessment concept that is of interest in education. The Doctor of Pharmacy program is one of the programs in which FA is usually implemented. This study aimed to describe the correlation between FA scores and summative assessment (SA) scores and to suggest possible key success factors that affect the effectiveness of FA.

METHODS: This study employed a retrospective design using mixed methods for data collection. Data in the semesters 1/2020 and 2/2020 of the Doctor of Pharmacy curriculum in a Thailand pharmacy school were used. Three sets of data were gathered, including the course information (e.g. FA methods, FA scores, and SA scores) from 38 records, self-reports from 326 students and 27 teachers, and 5 focus group discussions. The quantitative data were statistically analyzed using descriptive statistics and Pearson correlation, while the qualitative data were analyzed using a content analysis framework.

RESULTS: The analysis revealed five main methods that were used for FA, including individual quizzes, individual reports, individual skill assessments, group presentations, and group reports. Of all 38 courses, 29 (76.32%) had significant correlations between FA and SA scores at p-values < 0.05. The individual FA score was related to the correlation coefficient of the courses (p-value = 0.007), but the group FA score was not related (p-value = 0.081). In addition, only the frequency of individual quiz had a significant effect on the correlation coefficient. Moreover, the key success factors which affected the effectiveness of FA were divided into six themes, including the appropriate method, an effective reflection, frequency of assessment, the appropriate score, the adequate support system, and teacher knowledge management.

CONCLUSION: The subjects that used individual FA methods provided a significant correlation between FA and SA, while those who used group FA methods did not show a significant correlation. Additionally, the key success factors in this study were appropriate assessment methods, frequency of assessment, effective feedback, appropriate scoring, and a proper support system.

PMID:37131144 | DOI:10.1186/s12909-023-04232-1

BMC Bioinformatics. 2023 May 2;24(1):180. doi: 10.1186/s12859-023-05305-0.

ABSTRACT

BACKGROUND: Large-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies. Inference of the population structure with such sequencing data is fundamentally important. However, the ultra-dimensionality and complicated linkage disequilibrium patterns across the whole genome make it challenging to infer population structure using traditional principal component analysis based methods and software.

RESULTS: We present the ERStruct Python Package, which enables the inference of population structure using whole-genome sequencing data. By leveraging parallel computing and GPU acceleration, our package achieves significant improvements in the speed of matrix operations for large-scale data. Additionally, our package features adaptive data splitting capabilities to facilitate computation on GPUs with limited memory.

CONCLUSION: Our Python package ERStruct is an efficient and user-friendly tool for estimating the number of top informative principal components that capture population structure from whole genome sequencing data.

PMID:37131141 | DOI:10.1186/s12859-023-05305-0

BMC Geriatr. 2023 May 2;23(1):262. doi: 10.1186/s12877-023-03969-0.

ABSTRACT

BACKGROUND: Prediction of preoperative frailty risk in the emergency setting is a challenging issue because preoperative evaluation cannot be done sufficiently. In a previous study, the preoperative frailty risk prediction model used only diagnostic and operation codes for emergency surgery and found poor predictive performance. This study developed a preoperative frailty prediction model using machine learning techniques that can be used in various clinical settings with improved predictive performance.

METHODS: This is a national cohort study including 22,448 patients who were older than 75 years and visited the hospital for emergency surgery from the cohort of older patients among the retrieved sample from the Korean National Health Insurance Service. The diagnostic and operation codes were one-hot encoded and entered into the predictive model using the extreme gradient boosting (XGBoost) as a machine learning technique. The predictive performance of the model for postoperative 90-day mortality was compared with those of previous frailty evaluation tools such as Operation Frailty Risk Score (OFRS) and Hospital Frailty Risk Score (HFRS) using the receiver operating characteristic curve analysis.

RESULTS: The predictive performance of the XGBoost, OFRS, and HFRS for postoperative 90-day mortality was 0.840, 0.607, and 0.588 on a c-statistics basis, respectively.

CONCLUSIONS: Using machine learning techniques, XGBoost to predict postoperative 90-day mortality, using diagnostic and operation codes, the prediction performance was improved significantly over the previous risk assessment models such as OFRS and HFRS.

PMID:37131138 | DOI:10.1186/s12877-023-03969-0

BMC Pregnancy Childbirth. 2023 May 2;23(1):307. doi: 10.1186/s12884-023-05631-4.

ABSTRACT

BACKGROUND: Adverse neonatal outcomes are one of the most common causes of neonatal mortality and morbidity. Empirical evidence across the world shows that induction of labor potentiates adverse neonatal outcomes. In Ethiopia, there has been limited data that compares the frequency of adverse neonatal outcomes between induced and spontaneous labor.

OBJECTIVES: To compare the prevalence of adverse neonatal outcomes between induced and spontaneous labor and to determine associated factors among women who gave birth in public hospitals of Awi Zone, Northwest Ethiopia.

METHODS: A comparative cross-sectional study was conducted at Awi Zone public hospitals from May 1 to June 30, 2022. A simple random sampling technique was employed to select 788 (260 induced and 528 spontaneous) women. The collected data were analyzed using statistical package for social science (SPSS) software version 26. The Chi-square test and an independent t-test were used for categorical and continuous variables, respectively. A binary logistic regression was used to assess the association between the outcome and explanatory variables. In the bivariate analysis, a p-value ≤ 0.2 at a 95% confidence interval was used to consider the variables in the multivariate analysis. Finally, statistical significance was stated at a p-value of less than 0.05.

RESULT: The adverse neonatal outcomes among women who gave birth through induced labor were 41.1%, whereas spontaneous labor was 10.3%. The odds of adverse neonatal outcomes in induced labor were nearly two times higher than in spontaneous labor (AOR = 1.89, 95% CI: 1.11-3.22). No education (AOR = 2.00, 95% CI: 1.56, 6.44), chronic disease (AOR = 3.99, 95% CI: 1.87, 8.52), male involvement (AOR = 2.23, 95% CI: 1.23, 4.06), preterm birth (AOR = 9.83, 95% CI: 8.74, 76.37), operative delivery (AOR = 8.60, 95% CI: 4.63, 15.90), cesarean section (AOR = 4.17, 95% CI: 1.94, 8.95), and labor complications (AOR = 5.16, 95% CI: 2.90, 9.18) were significantly associated factors with adverse neonatal outcomes.

CONCLUSION AND RECOMMENDATION: Adverse neonatal outcomes in the study area were higher. Composite adverse neonatal outcomes were significantly higher in induced labor compared to spontaneous labor. Therefore, it is important to anticipate the possible adverse neonatal outcomes and plan management strategies while conducting every labor induction.

PMID:37131132 | DOI:10.1186/s12884-023-05631-4

BMC Med Res Methodol. 2023 May 2;23(1):109. doi: 10.1186/s12874-023-01937-1.

NO ABSTRACT

PMID:37131119 | DOI:10.1186/s12874-023-01937-1

Drug Alcohol Depend. 2023 Apr 14;247:109876. doi: 10.1016/j.drugalcdep.2023.109876. Online ahead of print.

ABSTRACT

BACKGROUND: Few studies examine the utility of the Cannabis Use Disorder Identification Test – Revised (CUDIT-R) in relation to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, (DSM-5) criteria for cannabis use disorder (CUD). This study assesses the performance of the CUDIT-R among a sample of Veterans with and without medical cannabis use.

METHODS: We approached and consented primary care patients presenting to one of three Department of Veterans Affairs (VA) Medical Centers. Veterans with at least monthly cannabis use and complete CUD data at baseline were included in this analysis (n=234). CUDIT-R scores were compared against Alcohol Use Disorder and Associated Disabilities Interview Schedule-5 (DSM-5) CUD as the standard to calculate measures of validity (sensitivity, specificity), identify optimal CUDIT-R cutoff values, and assess the diagnostic proficiency of the CUDIT-R using receiver operating characteristic (ROC) curves. We further stratified analyses by active medical cannabis card holder status and DSM-5 CUD severity (any, moderate, and severe).

RESULTS: Among the entire sample, 38.9% qualified for any DSM-5 CUD, with 10.7% and 3.0% meeting criteria for moderate and severe CUD, respectively. We identified optimal CUDIT-R scores at 10 for any DSM-5 CUD (sensitivity=0.58; specificity=0.80), at 12 for moderate CUD (sensitivity=0.72; specificity=0.82), and at 14 for severe CUD (sensitivity=0.71; specificity=0.87). ROC curves showed higher CUDIT-R validity among non-card holders compared with medical cannabis card holders.

CONCLUSION: The present study identified optimal CUDIT-R cutoff scores for Veterans who use cannabis. Varying DSM-5 validity measures inform the need for population-specific CUDIT-R cutoff values.

PMID:37130467 | DOI:10.1016/j.drugalcdep.2023.109876

J Plast Reconstr Aesthet Surg. 2023 Feb 26;81:99-104. doi: 10.1016/j.bjps.2023.02.025. Online ahead of print.

ABSTRACT

BACKGROUND: Breast reconstruction (BR) is an essential part of breast cancer treatment, and the DIEP flap is considered the gold standard reconstruction technique, which uses a free abdominal flap. Concerns have been raised regarding the effects of abdominoplasty on respiratory functions. This topic has not been addressed regarding donor-site closure of DIEP flaps. Our aim is to prospectively compare preoperative and postoperative spirometry in patients undergoing DIEP flap-based BR, investigating its impact on respiratory function.

MATERIALS AND METHODS: We enrolled 21 patients who received BR with DIEP flap in our institution, who underwent pulmonary function assessment by spirometry 1 month preoperatively and 1 year postoperatively. We assessed Forced Expiratory Volume in the first second (FEV1), Forced Vital Capacity (FVC), FEV1/FVC ratio, and Peak Expiratory Flow (PEF). Statistical analysis was performed using the paired samples test.

RESULTS: An improvement in the mean values of all 4 variables was found at 1 year from surgery. Namely, FEV1 improved by 0.1 L with a standard deviation (SD) of 0.39 L, FVC by 0.04 L with SD of 0.627, FEV1/FVC by 2.11 L with SD of 7.85 L, and PEF by 1.2 L with SD of 1.45 L. Only PEF was statistically significant [P = 0.001].

CONCLUSION: Our results suggest that DIEP flap BR does not negatively impact respiratory function. Although further knowledge is required, we confirm the possibility of considering the indication for abdominoplasty and DIEP flap reconstruction in patients with altered and reduced pulmonary function.

PMID:37130446 | DOI:10.1016/j.bjps.2023.02.025

Lung Cancer. 2023 Apr 19;180:107196. doi: 10.1016/j.lungcan.2023.107196. Online ahead of print.

ABSTRACT

BACKGROUND: Navigation bronchoscopy has seen rapid development in the past decade in terms of new navigation techniques and multi-modality approaches utilizing different techniques and tools. This systematic review analyses the diagnostic yield and safety of navigation bronchoscopy for the diagnosis of peripheral pulmonary nodules suspected of lung cancer.

METHODS: An extensive search was performed in Embase, Medline and Cochrane CENTRAL in May 2022. Eligible studies used cone-beam CT-guided navigation (CBCT), electromagnetic navigation (EMN), robotic navigation (RB) or virtual bronchoscopy (VB) as the primary navigation technique. Primary outcomes were diagnostic yield and adverse events. Quality of studies was assessed using QUADAS-2. Random effects meta-analysis was performed, with subgroup analyses for different navigation techniques, newer versus older techniques, nodule size, publication year, and strictness of diagnostic yield definition. Explorative analyses of subgroups reported by studies was performed for nodule size and bronchus sign.

RESULTS: A total of 95 studies (n = 10,381 patients; n = 10,682 nodules) were included. The majority (n = 63; 66.3%) had high risk of bias or applicability concerns in at least one QUADAS-2 domain. Summary diagnostic yield was 70.9% (95%-CI 68.4%-73.2%). Overall pneumothorax rate was 2.5%. Newer navigation techniques using advanced imaging and/or robotics(CBCT, RB, tomosynthesis guided EMN; n = 24 studies) had a statistically significant higher diagnostic yield compared to longer established techniques (EMN, VB; n = 82 studies): 77.5% (95%-CI 74.7%-80.1%) vs 68.8% (95%-CI 65.9%-71.6%) (p < 0.001).Explorative subgroup analyses showed that larger nodule size and bronchus sign presence were associated with a statistically significant higher diagnostic yield. Other subgroup analyses showed no significant differences.

CONCLUSION: Navigation bronchoscopy is a safe procedure, with the potential for high diagnostic yield, in particular using newer techniques such as RB, CBCT and tomosynthesis-guided EMN. Studies showed a large amount of heterogeneity, making comparisons difficult. Standardized definitions for outcomes with relevant clinical context will improve future comparability.

PMID:37130440 | DOI:10.1016/j.lungcan.2023.107196

Lasers Surg Med. 2023 May 2. doi: 10.1002/lsm.23675. Online ahead of print.

ABSTRACT

OBJECTIVE: A fractional 1064-nm picosecond laser is an efficient and safe treatment for atrophic acne scars. However, evidence of using a picosecond laser for atrophic posttraumatic and surgical scar therapy is lacking. This study aimed to evaluate the efficacy and safety of using a 1064-nm picosecond laser with a microlens array (MLA) for the treatment of atrophic posttraumatic and surgical scars.

METHODS: This was a prospective, intraindividual, single-blinded, randomized split-lesion-controlled trial. Twenty-five subjects with atrophic traumatic or surgical scars that existed for more than 1 year were enrolled. All atrophic scars were divided at the midline into two halves and randomly assigned to a treatment or control side. The treatment group was treated with a 1064-nm picosecond laser with an MLA handpiece (spot size: 6-8 mm, fluence: 1.0-1.2 J/cm² , repetition rate: 5 Hz, three passes) for 3 monthly sessions. The scar volumes were objectively measured using a three-dimensional (3D) photograph at baseline, 1 month after the first and second treatments, and 3 and 6 months after the final treatment. Subjective assessments were conducted by a blinded dermatologist and patients’ self-assessment to evaluate improvements at 3 months after the final treatment.

RESULTS: The treated sides exhibited a significant volume reduction, with statistically significant improvements over the control group at 1 month after the first and second treatments and at 3 months after the final treatment (p = 0.024, 0.005, and 0.019, respectively). At 3 months after the final treatment, a blinded dermatologist correctly identified the treated side in 24 of 25 patients (96%). The patients rated the improvements as excellent (>75%) and marked (50%-75%) in 36% and 48% of patients, respectively.

CONCLUSION: At 3 months, the 1064-nm picosecond laser with a fractionated MLA can significantly reduce the posttraumatic and postsurgical atrophic scar volume in patients with Fitzpatrick skin types III-V. Insufficient data preclude inferences regarding efficacy at 6 months.

PMID:37130437 | DOI:10.1002/lsm.23675