Tag: statistics

BMC Med Genomics. 2023 Mar 7;16(1):44. doi: 10.1186/s12920-023-01477-z.

ABSTRACT

INTRODUCTION: Gastric inhibitory polypeptide receptor (GIPR) encodes a G-protein coupled receptor for gastric inhibitory polypeptide (GIP), which was demonstrated to stimulate insulin secretion. Relation of GIPR gene variation to impaired insulin response has been suggested in previous studies. However, little information is available regarding GIPR polymorphisms and type 2 diabetes mellitus (T2DM). Hence, the aim of the study was to investigate single nucleotide polymorphisms (SNPs) in the promoter and coding regions of GIPR in Iranian T2DM patients.

MATERIALS AND METHODS: Two hundred subjects including 100 healthy and 100 T2DM patients were recruited in the study. Genotypes and allele frequency of rs34125392, rs4380143 and rs1800437 in the promoter, 5′ UTR and coding region of GIPR were investigated by RFLP-PCR and Nested-PCR.

RESULTS: Our finding indicated that rs34125392 genotype distribution was statistically different between T2DM and healthy groups (P = 0.043). In addition, distribution of T/- + -/- versus TT was significantly different between the both groups (P = 0.021). Moreover, rs34125392 T/- genotype increased the risk of T2DM (OR = 2.68, 95%CI = 1.203-5.653, P = 0.015). However, allele frequency and genotype distributions of rs4380143 and rs1800437 were not statistically different between the groups (P > 0.05). Multivariate analysis showed that the tested polymorphisms had no effect on biochemical variables.

CONCLUSION: We concluded that GIPR gene polymorphism is associated with T2DM. In addition; rs34125392 heterozygote genotype may increase the risk of T2DM. More studies with large sample size in other populations are recommended to show the ethnical relation of these polymorphisms to T2DM.

PMID:36882778 | DOI:10.1186/s12920-023-01477-z

BMC Surg. 2023 Mar 7;23(1):49. doi: 10.1186/s12893-023-01948-1.

ABSTRACT

PURPOSE: The purpose of this study is to compare the early results of patient-reported outcomes between two generations of a total knee system.

METHODS: Between June 2018 and April 2020, 121 first-generation, cemented TKAs (89 patients) and 123 s-generation, cemented TKAs (98 patients) were performed by a single surgeon. Demographic and surgical data were collected from all patients. Starting at the 6-month follow-up, patient-reported outcome measures Knee Injury and Osteoarthritis Outcome Score, Joint Reconstruction (KOOS-JR) and Knee Society (KS) clinical and radiographic scores were prospectively recorded. This study represents a retrospective review of these prospectively collected data.

RESULTS: There were no statistically significant differences between the two groups in terms of demographic variables such as age, body mass index, gender and race. KOOS-JR and Knee Society (KS) scores improved significantly (p < 0.001) from their preoperative values in both device generations. There were no differences, pre-operatively, between the two groups in terms of KOOS-JR, KS functional, KS objective, patient satisfaction, and expectation scores; however, there were statistically significant (p < 0.001) lower values of KOOS-JR and KS functional scores for first versus second generation at 6 months (81 vs. 89 and 69 vs. 74, respectively).

CONCLUSION: While significant improvement in KS objective, subjective, and patient satisfaction scores were noted with both knee systems, KOOS-JR and KS function scores were significantly higher at the early (6-month) follow-up in the second-generation group. Patients responded acutely to the design change as evidenced by significantly improved patient-reported outcome scores for the second generation.

PMID:36882774 | DOI:10.1186/s12893-023-01948-1

BMC Infect Dis. 2023 Mar 7;23(1):138. doi: 10.1186/s12879-023-08061-x.

ABSTRACT

PURPOSE: The commitment of multidisciplinary teams in antimicrobial stewardship programs (ASPs) is often inadequately considered, especially in surgical wards. We wanted to evaluate clinical, microbiological, and pharmacological outcomes before and after the implementation of an ASP in the Vascular Surgery ward of Fondazione IRCCS Policlinico San Matteo, a tertiary care hospital in Pavia, Italy.

METHODS: This was a quasi-experimental quality-improvement study. The antimicrobial stewardship activity was conducted twice a week for 12 months and consisted of both prospective audit and feedback of all the ongoing antimicrobial prescriptions by the infectious diseases’ consultants and educational meetings for the healthcare workers of the Vascular Surgery ward. For comparison between the study periods, Student t test (Mann-Whitney test for skewed distributions) was used for quantitative variables (ANOVA or Kruskall-Wallis for > 2 groups respectively), and Pearson’s chi-squared test (Fisher exact test where appropriate) for categorical variables. 2-tailed tests were used. P-value significance cut-off was 0.05.

RESULTS: During the 12-month intervention period, among a total number of 698 patients, 186 prescriptions were revised, mostly leading to de-escalating an ongoing antimicrobial therapy (39, 20.97%). A statistically significant reduction in isolates of carbapenem-resistant Pseudomonas aeruginosa (p-value 0.003) and the absence of Clostridioides difficile infections were reported. No statistically significant changes were observed in terms of length of stay and all-cause in-hospital mortality. A significant decrease in the administration of carbapenems (p-value 0.01), daptomycin (p-value < 0.01) and linezolid (p-value 0.43) was registered. A significant reduction in antimicrobial costs was also observed.

CONCLUSIONS: The implementation of a 12-month ASP brought significant clinical and economic results, highlighting the benefits of a multidisciplinary teamwork.

PMID:36882761 | DOI:10.1186/s12879-023-08061-x

BMC Health Serv Res. 2023 Mar 7;23(1):223. doi: 10.1186/s12913-023-09211-2.

ABSTRACT

BACKGROUND: The COVID-19 pandemic has highlighted human resource gaps and physician shortages in healthcare systems in New Brunswick (NB), as evidenced by multiple healthcare service interruptions. In addition, the New Brunswick Health Council gathered data from citizens on the type of primary care models (i.e. physicians in solo practice, physicians in collaborative practice, and collaborative practice with physicians and nurse practitioners) they use as their usual place of care. To add to their survey’s findings, our study aims to see how these different primary care models were associated with job satisfaction as reported by primary care providers.

METHODS: In total, 120 primary care providers responded to an online survey about their primary care models and job satisfaction levels. We used IBM’s “SPSS Statistics” software to run Chi-square and Fisher’s exact tests to compare job satisfaction levels between variable groups to determine if there were statistically significant variations.

RESULTS: Overall, 77% of participants declared being satisfied at work. The reported job satisfaction levels did not appear to be influenced by the primary care model. Participants reported similar job satisfaction levels regardless of if they practiced alone or in collaboration. Although 50% of primary care providers reported having symptoms of burnout and experienced a decline in job satisfaction during the COVID-19 pandemic, the primary care model was not associated with these experiences. Therefore, participants who reported burnout or a decline in job satisfaction were similar in all primary care models. Our study’s results suggest that the autonomy to choose a preferred model was important, since 45.8% of participants reported choosing their primary care models, based on preference. Proximity to family and friends and balancing work and family emerged as critical factors that influence choosing a job and staying in that job.

CONCLUSION: Primary care providers’ staffing recruitment and retention strategies should include the factors reported as determinants in our study. Primary care models do not appear to influence job satisfaction levels, although having the autonomy to choose a preferred model was reported as highly important. Consequently, it may be counterproductive to impose specific primary care models if one aims to prioritize primary care providers’ job satisfaction and wellness.

PMID:36882756 | DOI:10.1186/s12913-023-09211-2

Malar J. 2023 Mar 7;22(1):82. doi: 10.1186/s12936-023-04519-0.

ABSTRACT

BACKGROUND: Carriers of persistent asymptomatic Plasmodium falciparum infections constitute an infectious reservoir that maintains malaria transmission. Understanding the extent of carriage and characteristics of carriers specific to endemic areas could guide use of interventions to reduce infectious reservoir.

METHODS: In eastern Gambia, an all-age cohort from four villages was followed up from 2012 to 2016. Each year, cross-sectional surveys were conducted at the end of the malaria transmission season (January) and just before the start of the next one (June) to determine asymptomatic P. falciparum carriage. Passive case detection was conducted during each transmission season (August to January) to determine incidence of clinical malaria. Association between carriage at the end of the season and at start of the next one and the risk factors for this were assessed. Effect of carriage before start of the season on risk of clinical malaria during the season was also examined.

RESULTS: A total of 1403 individuals-1154 from a semi-urban village and 249 from three rural villages were enrolled; median age was 12 years (interquartile range [IQR] 6, 30) and 12 years (IQR 7, 27) respectively. In adjusted analysis, asymptomatic P. falciparum carriage at the end of a transmission season and carriage just before start of the next one were strongly associated (adjusted odds ratio [aOR] = 19.99; 95% CI 12.57-31.77, p < 0.001). The odds of persistent carriage (i.e. infected both in January and in June) were higher in rural villages (aOR = 13.0; 95% CI 6.33-26.88, p < 0.001) and in children aged 5-15 years (aOR = 5.03; 95% CI 2.47-10.23, p = < 0.001). In the rural villages, carriage before start of the season was associated with a lower risk of clinical malaria during the season (incidence risk ratio [IRR] 0.48, 95% CI 0.27-0.81, p = 0.007).

CONCLUSIONS: Asymptomatic P. falciparum carriage at the end of a transmission season strongly predicted carriage just before start of the next one. Interventions that clear persistent asymptomatic infections when targeted at the subpopulation with high risk of carriage may reduce the infectious reservoir responsible for launching seasonal transmission.

PMID:36882754 | DOI:10.1186/s12936-023-04519-0

BMC Med. 2023 Mar 8;21(1):88. doi: 10.1186/s12916-023-02798-7.

ABSTRACT

BACKGROUND: Understanding the effects of risk factor burden and genetic predisposition on the long-term risk of atrial fibrillation (AF) is important to improve public health initiatives. However, the 10-year risk of AF considering risk factor burden and genetic predisposition is unknown.

METHODS: A total of 348,904 genetically unrelated participants without AF at baseline from the UK were categorized into three groups: index ages 45 years (n = 84,206), 55 years (n=117,520), and 65 years (n=147,178). Optimal, borderline, or elevated risk factor burden was determined by body mass index, blood pressure, diabetes mellitus, alcohol consumption, smoking status, and history of myocardial infarction or heart failure. Genetic predisposition was estimated using the polygenic risk score (PRS), constructed using 165 predefined genetic risk variants. The combined effects of risk factor burden and PRS on the risk of incident AF in 10 years were estimated for each index age. Fine and Gray models were developed to predict the 10-year risk of AF.

RESULTS: The overall 10-year risk of AF was 0.67% (95% CI: 0.61-0.73%) for index age 45 years, 2.05% (95% CI: 1.96-2.13%) for index age 55 years, and 6.34% (95% CI: 6.21-6.46%) for index age 65 years, respectively. An optimal risk factor burden was associated with later AF onset regardless of genetic predisposition and sex (P < 0.001). Significant synergistic interactions were observed for risk factor burden with PRS at each index age (P < 0.05). Participants with an elevated risk factor burden and high PRS had the highest 10-year risk of AF in reference to those who had both an optimal risk factor burden and a low PRS. At younger ages, optimal risk burden and high PRS might also lead to later onset of AF, compared to the joint effect of elevated risk burden and low/intermediate PRS.

CONCLUSIONS: Risk factor burden together with a genetic predisposition is associated with the 10-year risk of AF. Our results may be helpful in selecting high-risk individuals for primary prevention of AF and facilitating subsequent health interventions.

PMID:36882748 | DOI:10.1186/s12916-023-02798-7

BMC Microbiol. 2023 Mar 7;23(1):60. doi: 10.1186/s12866-023-02799-9.

ABSTRACT

BACKGROUND: A common task in analyzing metatranscriptomics data is to identify microbial metabolic pathways with differential RNA abundances across multiple sample groups. With information from paired metagenomics data, some differential methods control for either DNA or taxa abundances to address their strong correlation with RNA abundance. However, it remains unknown if both factors need to be controlled for simultaneously.

RESULTS: We discovered that when either DNA or taxa abundance is controlled for, RNA abundance still has a strong partial correlation with the other factor. In both simulation studies and a real data analysis, we demonstrated that controlling for both DNA and taxa abundances leads to superior performance compared to only controlling for one factor.

CONCLUSIONS: To fully address the confounding effects in analyzing metatranscriptomics data, both DNA and taxa abundances need to be controlled for in the differential analysis.

PMID:36882742 | DOI:10.1186/s12866-023-02799-9

BMC Infect Dis. 2023 Mar 7;23(1):137. doi: 10.1186/s12879-023-08104-3.

ABSTRACT

BACKGROUND: During the novel coronavirus disease-2019 pandemic, a considerable number of pneumothorax (PNX)/pneumomediastinum (PNM) associated with COVID-19 have been reported, and the incidence is higher in critically ill patients. Despite using a protective ventilation strategy, PNX/PNM still occurs in patients on invasive mechanical ventilation (IMV). This matched case-control study aims to identify the risk factors and clinical characteristics of PNX/PNM in COVID-19.

METHODS: This retrospective study enrolled adult patients with COVID-19, admitted to a critical care unit from March 1, 2020, to January 31, 2022. COVID-19 patients with PNX/PNM were compared, in a 1-2 ratio, to COVID-19 patients without PNX/PNM, matched for age, gender, and worst National Institute of Allergy and Infectious Diseases ordinal scale. Conditional logistic regression analysis was performed to assess the risk factors for PNX/PNM in COVID-19.

RESULTS: 427 patients with COVID-19 were admitted during the period, and 24 patients were diagnosed with PNX/PNM. Body mass index (BMI) was significantly lower in the case group (22.8 kg/m² and 24.7 kg/m²; P = 0.048). BMI was statistically significant risk factor for PNX/PNM in univariate conditional logistic regression analysis [odds ratio (OR), 0.85; confidence interval (CI), 0.72-0.996; P = 0.044]. For patients on IMV support, univariate conditional logistic regression analysis showed the statistical significance of the duration from symptom onset to intubation (OR, 1.14; CI, 1.006-1.293; P = 0.041).

CONCLUSIONS: Higher BMI tended to show a protective effect against PNX/PNM due to COVID-19 and delayed application of IMV might be a contributive factor for this complication.

PMID:36882735 | DOI:10.1186/s12879-023-08104-3

BMC Infect Dis. 2023 Mar 7;23(1):141. doi: 10.1186/s12879-023-08009-1.

ABSTRACT

OBJECTIVE: Visceral leishmaniasis (VL) is an endemic parasitic disease in Latin America, and its clinical picture is aggravated in coinfections with the human immunodeficiency virus (HIV). The objective of this study was to investigate clinical factors and laboratory variables associated with VL relapse and death in VL/HIV coinfected patients.

METHODS: A prospective longitudinal study was conducted from January 2013 to July 2020 among 169 patients coinfected with VL and HIV. The outcomes investigated were the occurrence of VL relapse and death. Chi-square test, Mann-Whitney test and logistic regression models were used for statistical analysis.

RESULTS: The occurrence rates were 41.4% for VL relapse and 11.2% for death. Splenomegaly and adenomegaly were associated with the increased risk of VL relapse. Patients with VL relapse had higher levels of urea (p = .005) and creatinine (p < .001). Patients who died had lower red blood cell counts (p = .012), hemoglobin (p = .017) and platelets (p < .001). The adjusted model showed that antiretroviral therapy for more than 6 months was associated with a decrease in VL relapse, and adenomegaly was associated with an increase in VL relapse. In addition, edema, dehydration, poor general health status, and paleness were associated with an increase in hospital death.

CONCLUSION: The findings suggest that adenomegaly, antiretroviral therapy, and renal abnormalities can be associated with VL relapse, while hematological abnormalities, and clinical manifestations like paleness, and edema can be associated with an increased odds of hospital death.

TRIAL REGISTRATION NUMBER: The study was submitted to the Ethics and Research Committee of the Federal University of Maranhão (Protocol: 409.351).

PMID:36882732 | DOI:10.1186/s12879-023-08009-1

BMC Bioinformatics. 2023 Mar 7;24(1):87. doi: 10.1186/s12859-023-05185-4.

ABSTRACT

BACKGROUND: Variation in omics data due to intrinsic biological stochasticity is often viewed as a challenging and undesirable feature of complex systems analyses. In fact, numerous statistical methods are utilized to minimize the variation among biological replicates.

RESULTS: We demonstrate that the common statistics relative standard deviation (RSD) and coefficient of variation (CV), which are often used for quality control or part of a larger pipeline in omics analyses, can also be used as a metric of a physiological stress response. Using an approach we term Replicate Variation Analysis (RVA), we demonstrate that acute physiological stress leads to feature-wide canalization of CV profiles of metabolomes and proteomes across biological replicates. Canalization is the repression of variation between replicates, which increases phenotypic similarity. Multiple in-house mass spectrometry omics datasets in addition to publicly available data were analyzed to assess changes in CV profiles in plants, animals, and microorganisms. In addition, proteomics data sets were evaluated utilizing RVA to identify functionality of reduced CV proteins.

CONCLUSIONS: RVA provides a foundation for understanding omics level shifts that occur in response to cellular stress. This approach to data analysis helps characterize stress response and recovery, and could be deployed to detect populations under stress, monitor health status, and conduct environmental monitoring.

PMID:36882728 | DOI:10.1186/s12859-023-05185-4