Category: Statistics

Diagn Cytopathol. 2021 Oct 28. doi: 10.1002/dc.24898. Online ahead of print.

ABSTRACT

BACKGROUNDS: Liquid-based cytology (LBC) has begun to be used in non-gynecological samples such as endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). This study aims to investigate the diagnostic value of LBC in intrathoracic lymph nodes and lung lesions sampled with EBUS-TBNA.

METHODS: In total, 174 cases that underwent EBUS-TBNA between July 2020 and February 2021 were included (75 and 99 cases were prepared using conventional and LBC methods, respectively). The two groups were compared in terms of diagnostic categories, number of slides, cell blocks, slides per location, locations sampled, immunohistochemical studies, sensitivity, specificity, and diagnostic accuracy.

RESULTS: The percentages of malignant, suspicious for malignancy, benign, and non-diagnostic (ND) cases were 51.8%, 1.1%, 39.6%, and 7.5%, respectively. The LBC and conventional group (CG) had similar rates in the diagnostic categories, except for ND (3.0% and 13.3%, respectively). The sensitivity of LBC and CG were 90.4% and 85.7%, respectively. There were no differences in the specificity and diagnostic accuracy between groups. There was a statistically significant difference between groups in terms of the number of slides, number of slides per location, number of cell blocks, and locations sampled (p < .001, p < .001, p < .05, p < .05).

CONCLUSION: The LBC technique can be used for samples taken with EBUS-TBNA. Rapid fixation and the absence of artificial problems greatly reduce the rate of ND samples in LBC slides. Other important advantages are a lower number of slides to examine and a greater number of cell blocks.

PMID:34709736 | DOI:10.1002/dc.24898

Methods Mol Biol. 2022;2377:391-421. doi: 10.1007/978-1-0716-1720-5_22.

ABSTRACT

TnSeq, or sequencing of transposon insertion libraries, has proven to be a valuable method for probing the functions of genes in a wide range of bacteria. TnSeq has found many applications for studying genes involved in core functions (such as cell division or metabolism), stress response, virulence, etc., as well as to identify potential drug targets. Two of the most commonly used transposons in practice are Himar1, which inserts randomly at TA dinucleotides, and Tn5, which can insert more broadly throughout the genome. These insertions cause putative gene function disruption, and clones with insertions in genes that cannot tolerate disruption (in a given condition) are eliminated from the population. Deep sequencing can be used to efficiently profile the surviving members, with insertions in genes that can be inferred to be non-essential. Data from TnSeq experiments (i.e. transposon insertion counts at specific genomic locations) is inherently noisy, making rigorous statistical analysis (e.g. quantifying significance) challenging. In this chapter, we describe Transit, a Python-based software package for analyzing TnSeq data that combines a variety of data processing tools, quality assessment methods, and analytical algorithms for identifying essential (or conditionally essential) genes.

PMID:34709629 | DOI:10.1007/978-1-0716-1720-5_22

J Ultrasound Med. 2021 Oct 28. doi: 10.1002/jum.15858. Online ahead of print.

ABSTRACT

OBJECTIVES: To explore the diagnostic value of contrast-enhanced ultrasound (CEUS) combined with the Chinese Thyroid Imaging Reporting and Data System (C-TIRADS) for differentiation of benign and malignant thyroid nodules.

METHODS: A retrospective analysis of the conventional ultrasound and CEUS data of 388 nodules in 355 patients who had undergone thyroid nodule resection was conducted. All nodules had clear pathological results. The CEUS observation indexes included the enhancement degree in the arterial phase (no enhancement, scant punctate-linear enhancement, mild enhancement, moderate enhancement, and high enhancement) and wash-out patterns (rapid wash-out, slow wash-out, and isochronous wash-out). Chi-square test between groups and receiver operating characteristic curves (ROC) were used to determine the malignant (+1 point) and benign (-1 point) observation indexes that were statistically significant for the differentiation between benign and malignant thyroid nodules. The CEUS and C-TIRADS malignant and benign indexes were combined to score and draw the ROC curve, which was compared with the ROC curve scored by C-TIRADS alone to compare the diagnostic efficacy of the two methods for differentiating between benign and malignant thyroid nodules.

RESULTS: Among the CEUS observation indexes, mild enhancement and rapid wash-out were malignant indexes, while isochronous wash-out was a benign index. The best diagnostic cut-off value for the differentiation of benign and malignant thyroid nodules using the C-TIRADS score and the C-TIRADS and CEUS combined score (C-TIRADS + CEUS score) was 2. The sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) of the two methods were 79.97, 75.48, 82.9, 70.5%, and 89.7, 72.9, 83.3, 82.5%, respectively. The area under the curve values were 0.840 and 0.877 (P < .001), respectively.

CONCLUSIONS: The CEUS feature of mild enhancement in the arterial phase and rapid wash-out pattern are suggestive of malignancy and isochronous wash-out pattern is suggestive of benignity. The C-TIRADS + CEUS score has a higher value for distinguishing benign from malignant thyroid nodules than the C-TIRADS score alone.

PMID:34709672 | DOI:10.1002/jum.15858

J Thromb Thrombolysis. 2021 Oct 28. doi: 10.1007/s11239-021-02597-y. Online ahead of print.

ABSTRACT

Lipoprotein(a) (Lp(a)) is a prothrombotic and anti-fibrinolytic lipoprotein, whose role has not been clearly defined in the pathogenesis of coronavirus disease 2019 (COVID-19). In this prospective observational study, serum Lp(a) as well as outcomes were measured in 50 COVID-19 patients and 30 matched sick controls. Lp(a) was also assessed for correlation with a wide panel of biomarkers. Serum Lp(a) did not significantly differ between COVID-19 patients and sick controls, though its concentration was found to be significantly associated with severity of COVID-19 illness, including acute kidney failure stage (r = 0.380, p = 0.007), admission disease severity (r = 0.355, p = 0.013), and peak severity (r = 0.314; p = 0.03). Lp(a) was also positively correlated with interleukin (IL)-8 (r = 0.308; p = 0.037), fibrinogen (r = 0.344; p = 0.032) and creatinine (r = 0.327; p = 0.027), and negatively correlated with ADAMTS13 activity/VWF:Ag (r = – 0.335; p = 0.021); but not with IL-6 (r = 0.241; p = 0.106). These results would hence suggest that adverse outcomes in patients with COVID-19 may be aggravated by a genetically determined hyper-Lp(a) state rather than any inflammation induced elevations.

PMID:34709533 | DOI:10.1007/s11239-021-02597-y

J Neural Transm (Vienna). 2021 Oct 28. doi: 10.1007/s00702-021-02429-6. Online ahead of print.

ABSTRACT

Encephalopathy is a neurological complication of COVID-19. The objective of this exploratory study is to investigate the link between systemic inflammation and brain microstructural changes (measured by diffusion-weighted imaging) in patients with COVID-19 encephalopathy. 20 patients with COVID-19 encephalopathy (age: 67.3 [Formula: see text] 10.0 years; 90% men) hospitalized in the Geneva University Hospitals for a SARS-CoV-2 infection between March and May 2020 were included in this retrospective cohort study. COVID-19 encephalopathy was diagnosed following a comprehensive neurobiological evaluation, excluding common causes of delirium, such as hypoxemic or metabolic encephalopathy. We investigated the correlation between systemic inflammation (measured by systemic C-reactive protein (CRP)) and brain microstructural changes in radiologically normal white matter (measured by apparent diffusion coefficient (ADC)) in nine spatially widespread regions of the white matter previously associated with delirium. Systemic inflammation (CRP = 60.8 ± 50.0 mg/L) was positively correlated with ADC values in the anterior corona radiata (p = 0.0089), genu of the corpus callosum (p = 0.0064) and external capsule (p = 0.0086) after adjusting for patients’ age. No statistically significant association between CRP and ADC was found in the other six white matter regions. Our findings indicate high risk of white matter abnormalities in COVID-19 encephalopathy patients with high peripheral inflammatory markers, suggesting aggressive imaging monitoring may be warranted in these patients. Future studies should clarify a possible specificity of the spatial patterns of CRP-white matter microstructure association in COVID-19 encephalopathy patients and disentangle the role of individual cytokines on brain inflammatory mechanisms.

PMID:34709472 | DOI:10.1007/s00702-021-02429-6

J Immigr Minor Health. 2021 Oct 28. doi: 10.1007/s10903-021-01300-w. Online ahead of print.

ABSTRACT

We examined the effect of waist-to-hip ratio, body mass index (BMI), diet, and physical activity on cognitive functioning among Hispanic/Latina breast cancer survivors in a cross-sectional design study. Participants were 54 Hispanic/Latina breast cancer survivors and completed the NIH Toolbox Cognition Battery. Linear Regression Models tested if statistically significant correlations held with covariates. After controlling for covariates, moderate and hard physical activity were not associated with cognition. However, very hard physical activity was positively associated with faster processing speed (β = 0.56, p < 0.001) and composite cognition score (β = 0.36, p < 0.05). Total time (minutes) of moderate to very hard physical activity was positively associated with cognitive flexibility (β = 0.52, p < 0.001). Total caloric intake was positively associated with episodic memory (β = 0.35 p < 0.05). BMI and WHR were not associated with cognition. These findings showed positive association with engagement in more MVPA and harder intensity physical activity to better cognitive functioning among Hispanic/Latina breast cancer survivors.ClinicalTrials.gov NCT02780271.

PMID:34709529 | DOI:10.1007/s10903-021-01300-w

Clin Oral Investig. 2021 Oct 28. doi: 10.1007/s00784-021-04172-4. Online ahead of print.

ABSTRACT

OBJECTIVES: Possible impact of obesity on stage and grade of periodontitis has never been investigated before. This study aimed to examine the association between body mass index (BMI) and stage/grade of periodontitis per the current classification of periodontal diseases.

MATERIAL AND METHODS: A total of 142 patients (82 males/60 females) were included in this study. “2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions” was taken as basis to characterize the stage/grade of periodontitis. Age, gender, smoking status, and frequency of tooth brushing, and medical data of the patients including hypertension, hyperlipidemia, BMI, and diabetes mellitus were obtained from the patient’s hospital records. Obesity was assessed by BMI using the “World Health Organization” criteria. For estimating the association between BMI and periodontitis, logistic regression analysis was utilized.

RESULTS: BMI was statistically associated with clinical attachment loss (CAL), probing pocket depth (PPD), Plaque index (PI), stage and grade of periodontitis, and number of remaining teeth (p < 0.001, p < 0.05, p < 0.05, p < 0.05, p < 0.001, respectively). According to the multiple regression analysis results, those with BMI 25-29.9 were found to be at risk of being stage III-IV 3.977 times (95% CI: 1.831-8.640, p < 0.001) higher than those with BMI < 25, and similarly, those with BMI ≥ 30 were found to be at risk of being stage III-IV 4.062 times (95% CI: 1.315-12.549, p = 0.015) higher than those with BMI < 25. No relationship was found between obesity and grade of periodontitis according to multivariate analysis.

CONCLUSIONS: BMI increases the likelihood of stage III and stage IV periodontitis; however, it does not have an impact on the grade of periodontitis.

CLINICAL RELEVANCE: It seems that obesity is related to the severity of periodontitis.

PMID:34709456 | DOI:10.1007/s00784-021-04172-4

Arch Orthop Trauma Surg. 2021 Oct 28. doi: 10.1007/s00402-021-04231-1. Online ahead of print.

ABSTRACT

INTRODUCTION: The use of tranexamic acid (TXA) in hip fracture surgery remains inconclusive. The aim of the present meta-analysis was to assess the role of TXA use in hip fracture surgery, and attempt to disclose possible factors which might influence TXA efficacy and safety.

MATERIALS AND METHODS: A systematic computerized literature search was conducted to retrieve all randomized controlled trials (RCTs) and cohort studies regarding TXA use in hip fracture surgery. Overall efficacy and safety were evaluated. Then, subgroup and meta-regression analyses were conducted to disclose the influence of geographic area, fracture type, administration route, frequency and dosage of TXA, blood transfusion threshold, and follow-up duration on the overall effect.

RESULTS: Thirty-four RCTs and 11 cohort studies were included. Patients receiving TXA had a significant decrease in the need for blood transfusion, reduced total, intra-operative and post-operative blood loss, a decrease in pre- and postoperative hemoglobin difference, without increasing thromboembolic events risk. Subgroup analysis showed that topical TXA had a lower transfusion rate compared with controls, yet the result did not reach statistical significance. Also, TXA had similar efficacy and safety profiles in patients with different frequency and dosage of TXA.

CONCLUSION: Current evidence indicated that intravenous administration of TXA could significantly reduce blood transfusion and blood loss without increasing risk of thromboembolic events. The frequency and dosage of TXA might not alter the beneficial effect. The application of topical TXA should be cautious.

PMID:34709457 | DOI:10.1007/s00402-021-04231-1

JAMA Netw Open. 2021 Oct 1;4(10):e2131749. doi: 10.1001/jamanetworkopen.2021.31749.

ABSTRACT

IMPORTANCE: Adults receiving dialysis treatment have a higher likelihood of death when infected with SARS-CoV-2 than adults not receiving dialysis treatment. To date, the immune response of people receiving dialysis after SARS-CoV-2 vaccination has not been systematically discussed.

OBJECTIVE: To assess immunogenicity rates in people with end-stage kidney disease (ESKD) receiving SARS-CoV-2 vaccines, explore postvaccination potential risk factors for nonresponse, and assess whether receiving dialysis is associated with different antibody response rates compared with the nondialysis population.

DATA SOURCES: This systematic review and meta-analysis used articles from PubMed, Medline, and Embase published before July 30, 2021, as well as articles in the medRxiv preprint server.

STUDY SELECTION: Studies that evaluated the immunogenicity rate according to the postvaccine antibody response rate in patients with ESKD receiving dialysis were selected.

DATA EXTRACTION AND SYNTHESIS: The meta-analysis was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. A random-effects model was used. Two independent reviewers conducted the literature search and extracted the data.

MAIN OUTCOMES AND MEASURES: The primary outcome was the pooled antibody postvaccine response rates in individuals with ESKD. The secondary outcomes were pooled response rates in individuals receiving and not receiving dialysis. Subgroup analysis and meta-regression were conducted to identify the sources of heterogeneity.

RESULTS: A total of 32 studies were included. The overall immunogenicity rate of the dialysis group was 86% (95% CI, 81%-89%). Meta-regression showed a significant difference was detected in the postvaccine response rate on the basis of prevalence of diabetes (regression coefficient, -0.06; 95% CI, -0.10 to -0.02; P = .004). Compared with nondialysis controls, patients in the dialysis group had a lower response rate after the first (relative risk [RR], 0.61; 95% CI, 0.47-0.79; I2 = 70.2%) and second (RR, 0.88; 95% CI, 0.82-0.93; I2 = 72.2%) doses, with statistically significantly increased RR between first and second doses (P = .007).

CONCLUSIONS AND RELEVANCE: These findings suggest that the immunogenicity rate among patients receiving dialysis was 41% after the first dose and 89% after the second dose. Diabetes might be a risk factor for nonresponse in the dialysis population. Patients receiving dialysis had a poorer antibody response rate than did individuals not receiving dialysis, particularly after the first dose.

PMID:34709385 | DOI:10.1001/jamanetworkopen.2021.31749

Diabetologia. 2021 Oct 28. doi: 10.1007/s00125-021-05598-x. Online ahead of print.

ABSTRACT

AIMS/HYPOTHESIS: We aimed to assess whether general practices (GPs) using an electronic disease management program (DMP) with population overviews, including alerts when patients failed to receive guideline-recommended prescription medications, increased prescriptions of lipid-lowering drugs for patients with type 2 diabetes with no history of lipid-lowering treatment.

METHODS: This observational study included 165 GPs that reached a high level of use of the DMP in 2012 and a control group of 135 GPs who reached a high level of use in 2013 and, hence, who were less exposed to the DMP throughout 2012. A binary measure for having been prescribed and filled lipid-lowering drugs at any time within a 12-month exposure period was derived for all patients with type 2 diabetes who did not receive a prescription for lipid-lowering drugs in the baseline year prior to the study period (i.e. 2011). Results were derived using ORs from multivariate logistic regression analyses. Subgroup stratification based on age, sex, diabetes duration, deprivation status and Charlson Comorbidity Index (CCI) score was conducted and assessed. Placebo tests were carried out to assess bias from selection to treatment.

RESULTS: Patients who did not receive a prescription of lipid-lowering drugs in the year prior to being listed with GPs that used the DMP had statistically significant greater odds of receiving a prescription of lipid-lowering medications when compared with individuals who attended control GPs (OR 1.23 [95% CI 1.09, 1.38]). When the analysis period was shifted back by 2 years, no significant differences in lipid-lowering drug prescription between the two groups were found to occur, which indicates that these results were not driven by selection bias. Subgroup analyses showed that the increase in lipid-lowering drug prescriptions was primarily driven by changes among male participants (OR 1.32 [95% CI 1.12, 1.54]), patients aged 60-70 years (OR 1.40 [95% CI 1.13, 1.74]), patients with a diabetes duration of ≤5 years (OR 1.33 [95% CI 1.13, 1.56]), non-deprived patients (OR 1.25 [95% CI 1.08, 1.45]) and patients without comorbidities (CCI score = 0; OR 1.27 [95% CI 1.11, 1.45]).

CONCLUSIONS/INTERPRETATION: Access to population overviews using a DMP with alerts of clinical performance measures with regard to adhering to guideline-recommended prescription of medications can increase GP prescriptions of lipid-lowering drugs.

PMID:34709425 | DOI:10.1007/s00125-021-05598-x