Tag: statistics

BMC Bioinformatics. 2022 Aug 7;23(1):325. doi: 10.1186/s12859-022-04870-0.

ABSTRACT

BACKGROUND: The malaria risk prediction is currently limited to using advanced statistical methods, such as time series and cluster analysis on epidemiological data. Nevertheless, machine learning models have been explored to study the complexity of malaria through blood smear images and environmental data. However, to the best of our knowledge, no study analyses the contribution of Single Nucleotide Polymorphisms (SNPs) to malaria using a machine learning model. More specifically, this study aims to quantify an individual’s susceptibility to the development of malaria by using risk scores obtained from the cumulative effects of SNPs, known as weighted genetic risk scores (wGRS).

RESULTS: We proposed an SNP-based feature extraction algorithm that incorporates the susceptibility information of an individual to malaria to generate the feature set. However, it can become computationally expensive for a machine learning model to learn from many SNPs. Therefore, we reduced the feature set by employing the Logistic Regression and Recursive Feature Elimination (LR-RFE) method to select SNPs that improve the efficacy of our model. Next, we calculated the wGRS of the selected feature set, which is used as the model’s target variables. Moreover, to compare the performance of the wGRS-only model, we calculated and evaluated the combination of wGRS with genotype frequency (wGRS + GF). Finally, Light Gradient Boosting Machine (LightGBM), eXtreme Gradient Boosting (XGBoost), and Ridge regression algorithms are utilized to establish the machine learning models for malaria risk prediction.

CONCLUSIONS: Our proposed approach identified SNP rs334 as the most contributing feature with an importance score of 6.224 compared to the baseline, with an importance score of 1.1314. This is an important result as prior studies have proven that rs334 is a major genetic risk factor for malaria. The analysis and comparison of the three machine learning models demonstrated that LightGBM achieves the highest model performance with a Mean Absolute Error (MAE) score of 0.0373. Furthermore, based on wGRS + GF, all models performed significantly better than wGRS alone, in which LightGBM obtained the best performance (0.0033 MAE score).

PMID:35934714 | DOI:10.1186/s12859-022-04870-0

BMC Cardiovasc Disord. 2022 Aug 7;22(1):361. doi: 10.1186/s12872-022-02803-6.

ABSTRACT

BACKGROUND: Management of life-threatening arrhythmia can be incredibly challenging in advanced health systems. In sub-Saharan Africa (SSA), this is likely more challenging because of weak pre-hospital and in-hospital critical care systems. Little is known about life-threatening arrhythmia and their outcomes in SSA. The aim of this study was to examine the types and outcomes of arrhythmias among haemodynamically unstable patients presenting at a tertiary hospital in Accra-Ghana.

METHOD: This was a retrospective case series study conducted at the Korle-Bu Teaching Hospital (KBTH), Accra-Ghana. Medical records of patients who presented with or developed haemodynamically unstable arrhythmias within 24h of admission from January 2018 to December 2020 were reviewed. The demographic characteristics and clinical data including outcomes of patients were collected. Descriptive statistics were used and results presented in frequency tables.

RESULTS: A total of 42 patients with life-threatening arrhythmias were included. Haemodynamically unstable tachyarrhythmias were the most common arrhythmias found among the patients (66.7%). Approximately 52% of patients had structural heart diseases whereas 26.2% had no apparent underlying cause or predisposing factor. Cardioversion (52.4%), commonly electrical (63.6%), and transvenous pacemaker implantation (23.8%) were the common initial interventions. The majority of the patients (88.1%) survived and were discharged home.

CONCLUSION: Tachyarrhythmias are the most common haemodynamically unstable arrhythmias seen among patients presenting emergently in a leading tertiary hospital in Ghana. A high survival rate was observed and cannot be extrapolated to other healthcare settings in sub-Saharan Africa with limited resources to manage these clinical entities.

PMID:35934708 | DOI:10.1186/s12872-022-02803-6

J Plast Reconstr Aesthet Surg. 2022 Feb 27:S1748-6815(22)00120-6. doi: 10.1016/j.bjps.2022.02.041. Online ahead of print.

ABSTRACT

BACKGROUND: Neither anatomic nor functional descriptions exist of trunk/breast lymphedema following breast cancer treatment. Indocyanine green (ICG)-lymphangiography has been shown to characterize lymph channel dysfunction seen in lymphedema. We propose using ICG-lymphangiography to evaluate trunk and breast lymphedema following breast cancer surgery to characterize the regions affected via a novel, validated staging system.

METHODS: Patients undergoing revisional breast surgery with suspicion of upper extremity lymphedema between December 2014 and March 2020 were offered lymphangiography. The breast and lateral/anterior trunks were visualized and blindly evaluated using Koshima’s patterns of dermal backflow. Patients were then staged. A linear-weighted Cohen’s kappa statistic was calculated comparing each rated area and stage assignment.

RESULTS: Fifty-two sides (29 patients) were included. Eight sides underwent no treatment and were considered controls. No lymphedema was identified within this cohort. One patient (two sides) had no transit of ICG. Seventy-six percent of the non-controls had dermal backflow. This was seen in 67% of anterior trunks, 50% of lateral trunks, 50% of inframammary folds (IMFs), 43% of inferior breasts, and 5% of superior breasts. Cohen’s kappa for area agreement was 0.4117 ± 0.0535. Stage 0 was seen in 31 (±7)% of sides; stage 1: 21 (±1)%; stage 2: 22 (±5)%; stage 3: 18 (±4)%; stage 4: 5 (±1)%; and stage 5: 4 (±0). Cohen’s kappa for staging was 0.8109 ± 0.0868.

CONCLUSION: Following breast cancer surgery, lymphedema occurs throughout the trunk and breast. Severe dysfunction appears to be located around the inferior-lateral aspect of the breast and chest wall. Furthermore, the Pittsburgh Trunk Lymphedema Staging System is a validated measure of trunk and breast lymphedema.

PMID:35934664 | DOI:10.1016/j.bjps.2022.02.041

Pain Manag Nurs. 2022 Aug 4:S1524-9042(22)00124-2. doi: 10.1016/j.pmn.2022.05.005. Online ahead of print.

ABSTRACT

OBJECTIVES: This study aimed to evaluate the effectiveness of cognitive behavioral therapy (CBT) and mindfulness therapy (MT) for pain relief and quality of life (QOL) in patients with diabetic neuropathy.

REVIEW/ANALYSIS METHODS: Four databases were systematically searched from their respective inception dates to 29 June 2021. Relevant randomized controlled trials (RCTs) were screened and assessed for risk of bias. Eight RCTs evaluating CBT or MT were included. Statistical analysis was performed using Review Manager 5.4.

RESULTS: Eight RCTs involving 384 patients with painful diabetic neuropathy (PDN) tested psychological interventions, including three CBT and five MT studies. The results showed that patients’ pain severity (standardized mean difference [SMD] = -0.60, 95% confidence interval [CI; -0.93 to -0.27], P = .0003) and QOL (SMD = -0.43, 95% CI [-0.83 to -0.04], p = .03) were improved immediately after treatment. Besides, the pain intensity (SMD = -0.67, 95% CI [-1.37 to 0.03], p = .06), pain interference (SMD = -0.75, 95% CI [-1.20 to -0.30], p = .001) and depressive symptoms (SMD = -0.62, 95% CI [-0.96 to -0.28], p = .0003) were superior to the control group after follow up. The subgroup analysis results of different intervention type showed that the CBT group could immediately improve pain (SMD = -0.44, 95% CI [-0.78 to -0.10], p = .01) after treatment. However, there was no statistically significant difference in the CBT group after follow-up (SMD = -0.15, 95% CI [-0.52 to 0.22], p = .42).

CONCLUSIONS: Cognitive behavioral therapy or MT is effective for treating pain in patients with diabetic peripheral neuropathy, improving the QOL, and reducing depressive symptoms. However, large-scale, multi-centre, rigorously designed RCTs are needed to further verify the long-term effects.

PMID:35934662 | DOI:10.1016/j.pmn.2022.05.005

Cardiovasc Revasc Med. 2022 Jul 27:S1553-8389(22)00689-3. doi: 10.1016/j.carrev.2022.07.017. Online ahead of print.

ABSTRACT

OBJECTIVE: We sought to compare the clinical outcomes with provisional versus double-stenting strategy for left main (LM) bifurcation percutaneous coronary intervention (PCI).

BACKGROUND: Despite two recent randomized controlled trials (RCTs) and several observational reports, the optimal LM bifurcation PCI technique remains controversial.

METHODS: PubMed, Cochrane Central Register of Controlled-Trials (CENTRAL), Clinicaltrials.gov, International Clinical Trial Registry Platform were leveraged for studies comparing PCI bifurcation techniques for LM coronary lesions using second-generation drug eluting stents (DES). The primary outcome was major adverse cardiovascular events (MACE). Secondary outcomes of interest were all-cause mortality, cardiovascular mortality, myocardial infarction (MI), target vessel or lesion revascularization, and stent thrombosis.

RESULTS: Two RCTs and 10 observational studies with 7105 patients were included. Median follow-up duration was 42 months (IQR: 25.7). Double stenting was associated with a trend towards higher incidence of MACE (odds ratio [OR] 1.20; 95 % confidence interval [CI] 0.94 to 1.53) compared with provisional stenting. This was mainly driven by higher rates of target lesion revascularization (TLR) (OR 1.50; 95 % CI 1.07 to 2.11). There were no statistically significant differences in the incidence of all-cause mortality, cardiovascular mortality, MI, or stent thrombosis. On subgroup analysis according to the study type, provisional stenting was associated with lower MACE and TLR in observational studies, but not in RCTs.

CONCLUSION: For LM bifurcation PCI using second-generation DES, a provisional stenting strategy was associated with a trend towards lower incidence of MACE driven by statistically significant lower rates of TLR, compared with systematic double stenting. These differences were primarily driven by observational studies. Further RCTs are warranted to confirm these findings.

CONDENSED ABSTRACT: Despite the two recent randomized controlled trials (RCTs) EBC Main and DK-CRUSH-V, and several observational reports, the optimal LM bifurcation PCI technique remains controversial. We sought to compare the clinical outcomes with provisional versus double-stenting strategy for left main (LM) bifurcation percutaneous coronary intervention (PCI). Electronic databases were leveraged for studies comparing provisional versus double stenting PCI bifurcation techniques for LM coronary lesions using second-generation drug eluting stents (DES). Two RCTs and 10 observational studies with 7105 patients were included. Median follow-up duration was 42 months (IQR: 25.7). Double stenting was associated with a trend towards higher incidence of MACE (odds ratio [OR] 1.20; 95 % confidence interval [CI] 0.94 to 1.53) compared with provisional stenting. This was mainly driven by higher rates of target lesion revascularization (TLR) (OR 1.50; 95 % CI 1.07 to 2.11). There were no statistically significant differences in the incidence of all-cause mortality, cardiovascular mortality, MI, or stent thrombosis. On subgroup analysis according to the study type, provisional stenting was associated with lower MACE and TLR in observational studies, but not in RCTs. Further RCTs are warranted to confirm these findings.

PMID:35934644 | DOI:10.1016/j.carrev.2022.07.017

J Cyst Fibros. 2022 Aug 4:S1569-1993(22)00637-3. doi: 10.1016/j.jcf.2022.07.015. Online ahead of print.

ABSTRACT

RATIONAL: People with cystic fibrosis carrying residual function (RF) mutations are considered to have a mild disease course. This may influence caregivers and patients on how intensive the treatments should be.

OBJECTIVES: Characterize disease severity of patients carrying RF mutations, using the European CF Society Patient Registry (ECFSPR) data.

METHODS: Demographic, clinical characteristics, lung function and death probability of patients carrying at least one RF mutation were analyzed and compared to patients homozygous to minimal function mutations (MF).

MAIN RESULTS: Of the 44,594 eligible patients (median age 19.5 years, IQR 10-29.8), 6,636 (14.6%) carried RF mutations, and 37,958 (85.1%) MF mutations. Patients carrying RF mutations were older, diagnosed at a later age, had lower sweat chloride at diagnosis and better FEV1pp at each age group. However, their FEV1pp declined with age and rates of chronic Pseudomonas aeruginosa increased with age. A significant number of patients with RF had FEV1pp similar to patients with MF at each age group. 4.5% of RF patients were treated with oxygen and 2.61% had a lung transplant. With increasing age, 26.6% of RF patients were treated with pancreatic enzymes associated with a more severe lung disease. RF patients had shortened life spans, with mortality starting around the age of 20 years.

CONCLUSIONS: Patients carrying an RF mutations experience a decline of pulmonary function with age, leading to life-shortening. Standard of care therapies and augmenting CFTR function may improve their survival and quality of life.

PMID:35934641 | DOI:10.1016/j.jcf.2022.07.015

Arab J Gastroenterol. 2022 Aug 4:S1687-1979(22)00060-0. doi: 10.1016/j.ajg.2022.06.007. Online ahead of print.

ABSTRACT

BACKGROUND AND STUDY AIMS: Despite its wide availability, we do not have sufficient data aboutthe quality of colonoscopy in Egypt. In this study, we proposed 13 indicators to assess the quality of colonoscopy procedures in the included study centers aiming to attain a representative image of the quality of CS in Egypt.

PATIENTS AND METHODS: A multicenter prospective study was conducted between July and December 2020, which included all patients who underwent colonoscopy in the participating centers. The following were the proposed quality indicators: indications for colonoscopy, preprocedure clinical assessment, obtaining written informed consent, adequate colon preparation, sedation, cecal intubation rate (CIR), withdrawal time, adenoma detection rate (ADR), complication rate, photographic documentation, automated sterilization, regular infection control check, and well-equipped postprocedure recovery room.

RESULT: A total of 1,006 colonoscopy procedures were performed during the study duration in the included centers. Our analysis showed the following four indicators that were fulfilled in all centers: appropriate indications for colonoscopy, preprocedure assessment, written informed consent, and automated sterilization. However, photographic documentation and postprocedure follow-up room were fulfilled only in 57 %. Furthermore, 71 % of the centers performed regular infection control checks. Adequate colon preparation was achieved in 61 % of the procedures, 81 % of the procedures were performed under sedation, 95.4 % CIR, 11-min mean withdrawal time, 15 % ADR, and 0.1 % overall complication rate. Statistically significant factors affecting CIR were age > 40 years, high-definition endoscope, previous colon intervention, and rectal bleeding, whereas those affecting ADR were age > 40 years, the use of image enhancement, previous colon intervention, rectal bleeding, the use of water pump, and a withdrawal time of > 9 min.

CONCLUSION: Our study revealed the bright aspects of colonoscopy practice in Egypt, including high CIRs and low complication rates; conversely, ADR, bowel cleansing quality, and infection control measures should be improved.

PMID:35934640 | DOI:10.1016/j.ajg.2022.06.007

Reprod Biomed Online. 2022 Jun 17:S1472-6483(22)00418-7. doi: 10.1016/j.rbmo.2022.06.008. Online ahead of print.

ABSTRACT

RESEARCH QUESTION: Is the composition of the endometrial or vaginal microbiota associated with recurrent pregnancy loss (RPL)?

DESIGN: Endometrial and vaginal samples were collected from 47 women with two or more consecutive pregnancy losses and 39 healthy control women without a history of pregnancy loss, between March 2018 and December 2020 at Helsinki University Hospital, Helsinki, Finland. The compositions of the endometrial and vaginal microbiota, analysed using 16S rRNA gene amplicon sequencing, were compared between the RPL and control women, and between individual vaginal and endometrial samples. The mycobiota composition was analysed using internal transcribed spacer 1 amplicon sequencing for a descriptive summary. The models were adjusted for body mass index, age and parity. False discovery rate-corrected P-values (q-values) were used to define nominal statistical significance at q < 0.05.

RESULTS: Lactobacillus crispatus was less abundant in the endometrial samples of women with RPL compared with controls (mean relative abundance 17.2% versus 45.6%, q = 0.04). Gardnerella vaginalis was more abundant in the RPL group than in controls in both endometrial (12.4% versus 5.8%, q < 0.001) and vaginal (8.7% versus 5.7%, q = 0.002) samples. The individual vaginal and endometrial microbial compositions correlated strongly (R = 0.85, P < 0.001). Fungi were detected in 22% of the endometrial and 36% of the vaginal samples.

CONCLUSIONS: Dysbiosis of the reproductive tract microbiota is associated with RPL and may represent a novel risk factor for pregnancy losses.

PMID:35934639 | DOI:10.1016/j.rbmo.2022.06.008

Clin Colorectal Cancer. 2022 Jul 8:S1533-0028(22)00069-X. doi: 10.1016/j.clcc.2022.07.001. Online ahead of print.

ABSTRACT

In squamous cell anal canal neoplasms, persistent disease or recurrence after initial chemoradiotherapy are not the rule, yet their occurrence deserves to be analyzed to better identify prognostics factors. The aim of our study was to describe the patterns of failures of the initial treatment, their subsequent evolution and to identify prognostic factors in these relapsed patients. All patients with non-metastatic anal squamous cell carcinoma initially treated with curative intent at the Centre Antoine Lacassagne between 1999 and 2019, and who presented persistent disease or recurrence were analyzed. The median follow-up was 44 months. Univariate and multivariate analyses were performed to identify prognostic factors. From our database of 528 patients, 77 patients were eligible: 25 with persistent disease and 52 with recurrence after complete response. The median overall survival was 39 months (95% CI: 25.5-52.3 months) from the date of treatment failure. In univariate analysis, prognostic factors were gender, initial lymph node status, type of failure, response to treatment’s failure. In multivariate analysis, only female gender remained statistically significant (HR 0.43- P=0.016). 32% of patients with persistent disease had metastatic status. 17.3% and 5.8% of recurrences respectively occurred after three and five years of follow-up. Systematic imaging could be performed after initial treatment because of distant lesions in one third of patients with persistent disease. The follow-up should not be interrupted before five years, given the significant frequency of late recurrences. In multivariate analysis, only female gender was statistically significant. Stratified treatment based on prognostic factors could be envisaged, the details of which remain to be defined.

PMID:35934635 | DOI:10.1016/j.clcc.2022.07.001

J World Fed Orthod. 2022 Aug 4:S2212-4438(22)00039-X. doi: 10.1016/j.ejwf.2022.07.001. Online ahead of print.

ABSTRACT

BACKGROUND: To evaluate the reliability of a new instrument to clinically measure the anteroposterior relationship of the maxillary central incisors to the forehead.

METHODS: An analytical cross-sectional study using a sample of 84 (67% female and 33% male) young adult participants was conducted. Measurements were performed according to Element II of the Andrews’ Six Elements of Orofacial Harmony by assessing the horizontal distance between the facial axis point of the maxillary central incisor and the forehead’s anterior limit line. The instrument tested was a transparent plastic template having a leveling meter, reference lines, and an embedded millimeter ruler. Two orthodontists evaluated the sample twice with a minimum of a two-week interval between evaluations. The reliability was evaluated using the intraclass correlation coefficient. Repeated-measures ANOVA was also performed.

RESULTS: Good to excellent intra- and interexaminer agreement, with intraclass correlation coefficient values of 0.874 (95% confidence interval 0.800-0.921; P < 0.001) and 0.876 (95% confidence interval 0.739-0.948; P < 0.001), respectively, were calculated. There were no statistically significant differences between all the repeated measurements assessed (P = 0.820).

CONCLUSIONS: The instrument showed good to excellent reliability for determining the anteroposterior relationship of the maxillary central incisors to the forehead and could be used to help orthodontists and maxillofacial surgeons indirectly evaluate the anteroposterior position of the maxilla.

PMID:35934619 | DOI:10.1016/j.ejwf.2022.07.001