Category: Statistics

BMC Med Res Methodol. 2024 Jul 13;24(1):148. doi: 10.1186/s12874-024-02271-w.

ABSTRACT

We propose a compartmental model for investigating smoking dynamics in an Italian region (Tuscany). Calibrating the model on local data from 1993 to 2019, we estimate the probabilities of starting and quitting smoking and the probability of smoking relapse. Then, we forecast the evolution of smoking prevalence until 2043 and assess the impact on mortality in terms of attributable deaths. We introduce elements of novelty with respect to previous studies in this field, including a formal definition of the equations governing the model dynamics and a flexible modelling of smoking probabilities based on cubic regression splines. We estimate model parameters by defining a two-step procedure and quantify the sampling variability via a parametric bootstrap. We propose the implementation of cross-validation on a rolling basis and variance-based Global Sensitivity Analysis to check the robustness of the results and support our findings. Our results suggest a decrease in smoking prevalence among males and stability among females, over the next two decades. We estimate that, in 2023, 18% of deaths among males and 8% among females are due to smoking. We test the use of the model in assessing the impact on smoking prevalence and mortality of different tobacco control policies, including the tobacco-free generation ban recently introduced in New Zealand.

PMID:39003462 | DOI:10.1186/s12874-024-02271-w

Plant Methods. 2024 Jul 13;20(1):103. doi: 10.1186/s13007-024-01210-6.

ABSTRACT

BACKGROUND: Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads. Existing workflows predominantly cater to phylogenetic inference, leaving a gap in user-friendly tools for genotyping analysis based on capture methods. In response to these challenges, we have developed GeCKO (Genotyping Complexity Knocked-Out). To assess the effectiveness of combining target enrichment capture with GeCKO, we conducted a case study on durum wheat domestication history, involving sequencing, processing, and analyzing variants in four relevant durum wheat groups.

RESULTS: GeCKO encompasses four distinct workflows, each designed for specific steps of genomic data processing: (i) read demultiplexing and trimming for data cleaning, (ii) read mapping to align sequences to a reference genome, (iii) variant calling to identify genetic variants, and (iv) variant filtering. Each workflow in GeCKO can be easily configured and is executable across diverse computational environments. The workflows generate comprehensive HTML reports including key summary statistics and illustrative graphs, ensuring traceable, reproducible results and facilitating straightforward quality assessment. A specific innovation within GeCKO is its ‘targeted remapping’ feature, specifically designed for efficient treatment of targeted enrichment capture data. This process consists of extracting reads mapped to the targeted regions, constructing a smaller sub-reference genome, and remapping the reads to this sub-reference, thereby enhancing the efficiency of subsequent steps.

CONCLUSIONS: The case study results showed the expected intra-group diversity and inter-group differentiation levels, confirming the method’s effectiveness for genotyping and analyzing genetic diversity in species with complex genomes. GeCKO streamlined the data processing, significantly improving computational performance and efficiency. The targeted remapping enabled straightforward SNP calling in durum wheat, a task otherwise complicated by the species’ large genome size. This illustrates its potential applications in various biological research contexts.

PMID:39003455 | DOI:10.1186/s13007-024-01210-6

BMC Public Health. 2024 Jul 13;24(1):1870. doi: 10.1186/s12889-024-19364-2.

ABSTRACT

Despite domestic violence and related homicides perpetrated by partners and/or in-laws being a significant public health problem in India, there are no reliable and valid instruments to identify and intervene with women in domestic violence relationships. Continued domestic violence can escalate to severe, near-lethal, or lethal violence or homicide. The Danger Assessment (DA) is a risk assessment instrument designed to assess the likelihood of severe, near-lethal, or lethal violence in abusive relationships. However, the DA is not designed to determine the risk of future severe, near-lethal, or lethal violence by in-laws. In-law abuse plays a significant role in domestic violence-related homicides in India and other countries with similar cultural norms. This study addressed this gap by developing the Danger Assessment for in-laws (DA-L) to assess risk from in-laws, alongside the Danger Assessment for Women in India (DA-WI) to assess risk from partners. The study also examined the psychometric properties of the DA-L and DA-WI. Longitudinal data from 150 women in India were used to measure the reliability and validity of the two versions of the DA. The original DA items and additional risk items were examined using relative risk ratios for their relationship with severe violence at three-month follow-ups. Predictive validity was tested with the receiver operating characteristic curve. The study resulted in reliable and valid measures (11 items DA-L and 26-items DA-WI) of risk. The versions of the DA can be useful for practitioners in India and those working with Indian women in the US and other countries. The DAs can be used for identifying women in domestic violence relationships who are at risk for future severe domestic violence and guide the provision of tailored safety plans.

PMID:39003451 | DOI:10.1186/s12889-024-19364-2

J Neuroeng Rehabil. 2024 Jul 13;21(1):118. doi: 10.1186/s12984-024-01416-8.

ABSTRACT

BACKGROUND: How the joints exactly move and interact and how this reflects PD-related gait abnormalities and the response to dopaminergic treatment is poorly understood. A detailed understanding of these kinematics can inform clinical management and treatment decisions. The aim of the study was to investigate the influence of different gait speeds and medication on/off conditions on inter-joint coordination, as well as kinematic differences throughout the whole gait cycle in well characterized pwPD.

METHODS: 29 controls and 29 PD patients during medication on, 8 of them also during medication off walked a straight walking path in slow, preferred and fast walking speeds. Gait data was collected using optical motion capture system. Kinematics of the hip and knee and coordinated hip-knee kinematics were evaluated using Statistical Parametric Mapping (SPM) and cyclograms (angle-angle plots). Values derived from cyclograms were compared using repeated-measures ANOVA for within group, and ttest for between group comparisons.

RESULTS: PD gait differed from controls mainly by lower knee range of motion (ROM). Adaptation to gait speed in PD was mainly achieved by increasing hip ROM. Regularity of gait was worse in PD but only during preferred speed. The ratios of different speed cyclograms were smaller in the PD groups. SPM analyses revealed that PD participants had smaller hip and knee angles during the swing phase, and PD participants reached peak hip flexion later than controls. Withdrawal of medication showed an exacerbation of only a few parameters.

CONCLUSIONS: Our findings demonstrate the potential of granular kinematic analyses, including > 1 joint, for disease and treatment monitoring in PD. Our approach can be extended to further mobility-limiting conditions and other joint combinations.

TRIAL REGISTRATION: The study is registered in the German Clinical Trials Register (DRKS00022998, registered on 04 Sep 2020).

PMID:39003450 | DOI:10.1186/s12984-024-01416-8

J Cardiothorac Surg. 2024 Jul 13;19(1):441. doi: 10.1186/s13019-024-02878-6.

ABSTRACT

BACKGROUND: Deep venous thrombosis (DVT) is a serious public health issue that threatens human health and economic development. Presently, differences in the prevalence of DVT among individuals from different nationalities, residents of high-altitude areas, and those consuming any special diet are unknown. Therefore, we aimed to elucidate the prevalence of and the associated risk factors for DVT in hospitalized patients in the plateau areas.

METHODS: The subjects were hospitalized patients in three grade III-a hospitals in the Qinghai Province, China, during January-October 2020. The demographic, clinical, and laboratory data were collected at admission, and ultrasonography of the bilateral lower extremities was performed. The hospital stay-duration was recorded at the time of discharge.

RESULTS: A total of 3432 patients were enrolled, of which 159 (4.60%) were diagnosed with DVT. The age of > 50 years (OR = 2.434, 95% CI: 1.521-3.894252, P < 0.001), residence altitude of ≥ 3000 m (OR = 2.346, 95% CI: 1.239-4.440, P = 0.009), D-dimer level of ≥ 0.5 mg/L (OR = 2.211, 95% CI: 1.547-3.161, P < 0.001), presence of comorbidities (OR = 1.904, 95% CI: 1.386-2.705, P < 0.001), a history of varicose veins (OR = 1.990, 95% CI: 0.959-4.128, P = 0.045), and current medications (OR = 2.484, 95% CI: 1.778-3.471, P < 0.001) were identified as risk factors for DVT in these plateau areas.

CONCLUSION: The prevalence of DVT in the hospitalized patients of the studied plateau areas was 4.60%. We recommend considering individualized risk stratification (age > 50 years, residence altitude ≥ 3000 m, a history of varicose veins, D-dimer level ≥ 0.5 mg/L, current medications, and comorbidities) for patients at the time of admission.

PMID:39003445 | DOI:10.1186/s13019-024-02878-6

BMC Cardiovasc Disord. 2024 Jul 13;24(1):357. doi: 10.1186/s12872-024-04017-4.

ABSTRACT

BACKGROUND: The epidemiological distribution of functional mitral regurgitation (FMR) in heart failure (HF) and mildly reduced ejection fraction (HFmrEF) patients and its impact on outcomes remains unclear. We attempt to investigate the prognosis of FMR in patients with HFmrEF.

METHODS: The HF center registry study is a prospective, single, observational study conducted at the Second Affiliated Hospital of Shenzhen University, where 2330 patients with acute HF (AHF) were enrolled and 890 HFmrEF patients were included in the analysis. The patients were stratified into three categories based on the severity of FMR: none/mild, moderate, and moderate-to-severe/severe groups. Subsequently, a comparison of the clinical characteristics among these groups was conducted, along with an assessment of the incidence of the primary endpoint (comprising all-cause mortality and readmission for HF) during a one-year follow-up period.

RESULTS: The one-year follow-up results indicated that the primary composite endpoint occurrence rates in the three groups were 23.5%, 32.9%, and 36.5%, respectively. The all-cause mortality rates in the three groups were 9.3%, 13.7%, and 16.4% respectively. Survival analysis demonstrated a statistically significant difference in the occurrence rates of the primary composite endpoint and all-cause mortality among the three groups (P < 0.05). Multifactor Cox regression revealed that moderate FMR and moderate-to-severe/severe FMR were independent risk factors for adverse clinical prognosis in HFmrEF patients, with hazard ratios and 95% confidence intervals of 1.382 (1.020-1.872, P = 0.037) and 1.546 (1.092-2.190, P = 0.014) respectively.

CONCLUSIONS: Moderate FMR and moderate-to-severe/severe FMR independently predict an unfavorable prognosis in patients with HFmrEF.

PMID:39003444 | DOI:10.1186/s12872-024-04017-4

BMC Cancer. 2024 Jul 13;24(1):838. doi: 10.1186/s12885-024-12615-w.

ABSTRACT

BACKGROUND: The National Comprehensive Cancer Network (NCCN) guideline recommends consideration of weekly cisplatin as an alternative option for patients with head and neck cancer undergoing definitive chemoradiation. However, in a recent phase III trial (ConCERT), 20% of patients treated with weekly cisplatin could not receive a total of 200 mg/m², and the association of low adherence to weekly cisplatin and cancer control outcomes remains unclear. To fill this knowledge gap, we performed an observational cohort study of patients with head and neck cancer undergoing definitive chemoradiation with weekly cisplatin.

METHODS: Our institutional database was queried for patients with non-metastatic head and neck cancer who underwent definitive chemoradiation with weekly cisplatin (40 mg/m²) between November 2007 and April 2023. Adherence to weekly cisplatin was defined as receiving at least 5 cycles with a total cumulative dose of 200 mg/m². Survival outcomes were evaluated using Kaplan-Meier method, log-rank tests, Cox proportional hazard multivariable (MVA) analyses. Logistic MVA was performed to identify variables associated with low adherence to weekly cisplatin. Fine-Gray MVA was performed to analyze failure outcomes with death as a competing event.

RESULTS: Among 119 patients who met our criteria, 51 patients (42.9%) had low adherence to weekly cisplatin. Median follow up was 19.8 months (interquartile range 8.8-65.6). Low adherence to weekly cisplatin was associated with worse overall survival (adjusted hazards ratio [aHR] 2.94, 95% confidence interval [CI] 1.58-5.47, p < 0.001) and progression-free survival (aHR 2.32, 95% CI 1.29-4.17, p = 0.005). It was also associated with worse distant failure (aHR 4.55, 95% CI 1.19-17.3, p = 0.03), but not locoregional failure (aHR 1.61, 95% CI 0.46-5.58, p = 0.46). KPS < 90 was the only variable associated with low adherence to weekly cisplatin (adjusted odds ratio [aOR] 2.67, 95% CI 1.10-6.65, p = 0.03).

CONCLUSION: Our study suggested that over 40% of patients underwent fewer than 5 weekly cisplatin cycles and that low adherence to weekly cisplatin was an independent, adverse prognostic factor for worse survival and distant failure outcomes. Those with reduced adherence to weekly cisplatin were more likely to have poor performance status. Further studies are warranted to improve the adherence to chemotherapy and outcomes.

PMID:39003442 | DOI:10.1186/s12885-024-12615-w

J Robot Surg. 2024 Jul 13;18(1):283. doi: 10.1007/s11701-024-02044-z.

ABSTRACT

The robotic approach improves the feasibility of minimally invasive colectomy even where there may be an anatomic challenge with laparoscopy. Whether a failure in completing colectomy with this newer technology is associated with worse consequences needs to be considered when evaluating the relative benefit of robotic colectomy. The aim of this study is to evaluate rates of conversion to open surgery after robotic and laparoscopic colectomy and whether outcomes after conversion vary after the two techniques since this has not been well studied. From the American College of Surgeons (ACS) – National Surgical Quality Improvement Program (NSQIP) (2015-2016), patients who underwent elective minimally invasive colectomy were identified. Converted robotic were compared to laparoscopic procedures for patient demographics, co-morbidities; primary procedure and diagnosis, prolonged operation and postoperative complications. Of 36,046 colectomy procedures, 30,808 (85.5%) were laparoscopic, while 5238 (14.5%) were robotic-assisted. There were 3271 (9.1%) conversions to open surgery (laparoscopic: 2959 [9.6%]; robotic: 312 [6%]). Thirty-day postoperative surgical site infection, anastomotic leak, ileus, sepsis, bleeding requiring transfusion, urinary tract infection, reoperation; pulmonary, renal, cardiac/cerebrovascular complications; readmission, hospital stay, and mortality, were similar between the two groups. However, deep vein thrombosis/pulmonary embolism was higher after robotic conversion (4.5% vs. 2.2%, p = 0.01). Conversion was lower after robotic when compared to laparoscopic colectomy. Converted patients had similar outcomes except for vein thromboembolism which was higher after robotic surgery. Robotic technology seems to improve the feasibility of minimally invasive surgery without negatively affecting safety and efficacy even when conversion is required.

PMID:39003434 | DOI:10.1007/s11701-024-02044-z

Eye (Lond). 2024 Jul 13. doi: 10.1038/s41433-024-03231-w. Online ahead of print.

ABSTRACT

PURPOSE: This study aimed to evaluate the accuracy of information that patients can obtain from large language models (LLMs) when seeking answers to common questions about choroidal melanoma.

METHODS: Comparative study comparing frequently asked questions from choroidal melanoma patients and queried three major LLMs-ChatGPT 3.5, Bing AI, and DocsGPT. Answers were reviewed by three ocular oncology experts and scored as accurate, partially accurate, or inaccurate. Statistical analysis compared the quality of responses across models.

RESULTS: For medical advice questions, ChatGPT gave 92% accurate responses compared to 58% for Bing AI and DocsGPT. For pre/post-op questions, ChatGPT and Bing AI were 86% accurate while DocsGPT was 73% accurate. There were no statistically significant differences between models. ChatGPT responses were the longest while Bing AI responses were the shortest, but length did not affect accuracy. All LLMs appropriately directed patients to seek medical advice from professionals.

CONCLUSION: LLMs show promising capability to address common choroidal melanoma patient questions at generally acceptable accuracy levels. However, inconsistent, and inaccurate responses do occur, highlighting the need for improved fine-tuning and oversight before integration into clinical practice.

PMID:39003430 | DOI:10.1038/s41433-024-03231-w

Mol Psychiatry. 2024 Jul 14. doi: 10.1038/s41380-024-02665-8. Online ahead of print.

ABSTRACT

Genetics research has potential to alleviate the burden of mental disorders in low- and middle-income-countries through identification of new mechanistic pathways which can lead to efficacious drugs or new drug targets. However, there is currently limited genetics data from Africa. The Uganda Genome Resource provides opportunity for psychiatric genetics research among underrepresented people from Africa. We aimed at determining the prevalence and correlates of major depressive disorder (MDD), suicidality, post-traumatic stress disorder (PTSD), alcohol abuse, generalised anxiety disorder (GAD) and probable attention-deficit hyperactivity disorder (ADHD) among participants of the Uganda Genome Resource. Standardised tools assessed for each mental disorder. Prevalence of each disorder was calculated with 95% confidence intervals. Multivariate logistic regression models evaluated the association between each mental disorder and associated demographic and clinical factors. Among 985 participants, prevalence of the disorders were: current MDD 19.3%, life-time MDD 23.3%, suicidality 10.6%, PTSD 3.1%, alcohol abuse 5.7%, GAD 12.9% and probable ADHD 9.2%. This is the first study to determine the prevalence of probable ADHD among adult Ugandans from a general population. We found significant association between sex and alcohol abuse (adjusted odds ratio [AOR] = 0.26 [0.14,0.45], p < 0.001) and GAD (AOR = 1.78 [1.09,2.49], p = 0.019) respectively. We also found significant association between body mass index and suicidality (AOR = 0.85 [0.73,0.99], p = 0.041), alcohol abuse (AOR = 0.86 [0.78,0.94], p = 0.003) and GAD (AOR = 0.93 [0.87,0.98], p = 0.008) respectively. We also found a significant association between high blood pressure and life-time MDD (AOR = 2.87 [1.08,7.66], p = 0.035) and probable ADHD (AOR = 1.99 [1.00,3.97], p = 0.050) respectively. We also found a statistically significant association between tobacco smoking and alcohol abuse (AOR = 3.2 [1.56,6.67], p = 0.002). We also found ever been married to be a risk factor for probable ADHD (AOR = 2.12 [0.88,5.14], p = 0.049). The Uganda Genome Resource presents opportunity for psychiatric genetics research among underrepresented people from Africa.

PMID:39003415 | DOI:10.1038/s41380-024-02665-8