Category: Statistics

Mol Ecol Resour. 2024 Apr 26:e13964. doi: 10.1111/1755-0998.13964. Online ahead of print.

ABSTRACT

Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop an ultrafast and memory-efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL’s efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.

PMID:38666432 | DOI:10.1111/1755-0998.13964

J Chem Theory Comput. 2024 Apr 26. doi: 10.1021/acs.jctc.4c00251. Online ahead of print.

ABSTRACT

An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate importance sampling in free energy simulations. The method achieves enhanced sampling from Hamiltonian replica exchange within a dual topology framework while utilizing new smoothstep softcore potentials. A common sampling problem encountered in lead optimization is the functionalization of aromatic rings that exhibit distinct conformational preferences when interacting with the protein. It is difficult to converge the distribution of ring conformations due to the long time scale of ring flipping events; however, the ACES method addresses this issue by modeling the syn and anti ring conformations within a dual topology. ACES thereby samples the conformer distributions by alchemically tunneling between states, as opposed to traversing a physical pathway with a high rotational barrier. We demonstrate the use of ACES to overcome conformational sampling issues involving ring flipping in ML300-derived noncovalent inhibitors of SARS-CoV-2 Main Protease (M^pro). The demonstrations explore how the use of replica exchange and the choice of softcore selection affects the convergence of the ring conformation distributions. Furthermore, we examine how the accuracy of the calculated free energies is affected by the degree of phase space overlap (PSO) between adjacent states (i.e., between neighboring λ-windows) and the Hamiltonian replica exchange acceptance ratios. Both of these factors are sensitive to the spacing between the intermediate states. We introduce a new method for choosing a schedule of λ values. The method analyzes short “burn-in” simulations to construct a 2D map of the nonlocal PSO. The schedule is obtained by optimizing an alchemical pathway on the 2D map that equalizes the PSO between the λ intervals. The optimized phase space overlap λ-spacing method (Opt-PSO) leads to more numerous end-to-end single passes and round trips due to the correlation between PSO and Hamiltonian replica exchange acceptance ratios. The improved exchange statistics enhance the efficiency of ACES method. The method has been implemented into the FE-ToolKit software package, which is freely available.

PMID:38666430 | DOI:10.1021/acs.jctc.4c00251

Breastfeed Med. 2024 Apr 26. doi: 10.1089/bfm.2024.0041. Online ahead of print.

ABSTRACT

Background: Breast milk is vital for the growth and development of preterm infants. However, in Neonatal Intensive Care Units (NICUs), mothers often encounter significant challenges in breastfeeding. Objective: This study aims to systematically evaluate the barriers to breastfeeding in NICUs, thereby providing evidence-based support for clinical practices. Methods: A comprehensive search was conducted in the Cochrane Library, PubMed, Web of Science, Embase, and Scopus databases, up to September 2023. Meta-analysis was performed using Stata 15.0, applying fixed or random effects models to calculate odds ratios (OR) and their 95% confidence intervals (CI). Study quality was assessed using the Newcastle-Ottawa Scale for cases and cohorts and the Agency for Healthcare Research and Quality standards for cross-sectional studies. Heterogeneity was evaluated using Cochran’s chi-squared test (Cochran’s Q) and I² statistics, and publication bias was assessed through funnel plots and symmetry tests. Results: A total of 32 studies were included, encompassing 96,053 preterm infants. The main barriers to breastfeeding in preterm infants included: low gestational age (OR = 1.36, 95% CI: 1.06-1.75), lower maternal education (OR = 1.64, 95% CI: 1.39-1.93), insufficient breast milk (OR = 2.09, 95% CI: 1.39-1.93), multiple births (OR = 1.615, 95% CI: 1.18-2.210), smoking (OR = 2.906, 95% CI: 2.239-3.771), and single motherhood (OR = 1.439, 95% CI: 1.251-1.654). Conclusion: This study underscores the need for individualized breastfeeding support strategies in NICUs, taking into account the diverse backgrounds of mothers. Future research should focus on unraveling the underlying mechanisms affecting breastfeeding in preterm infants, with the goal of enhancing breastfeeding rates and improving developmental outcomes.

PMID:38666420 | DOI:10.1089/bfm.2024.0041

J Adv Nurs. 2024 Apr 26. doi: 10.1111/jan.16198. Online ahead of print.

ABSTRACT

AIM: To examine healthcare providers’ extent of and perceived barriers and facilitators to screening for intimate partner violence in pregnant women attending prenatal clinics.

DESIGN: Cross-sectional descriptive design was used to collect data from 130 healthcare providers.

METHODS: Seventeen healthcare providers from 17 prenatal clinics in Kanungu district, Uganda, were recruited via convenience sampling to participate in an online survey implementing a modified Normalization Measure Development instrument. Data were collected between February 2023 and March 2023 (02/8/2023 to 03/12/2023) and analysed using descriptive and Mann-Whitney U test and chi-square tests.

RESULTS: Slightly more than half (56%) of healthcare providers report screening pregnant women for intimate partner violence. There was a statistically significant relationship between healthcare providers screening for intimate partner violence and having previous training on intimate partner violence screening. The only barrier to screening identified was a lack of understanding of how intimate partner violence screening affects the nature of participant’s own work. There were numerous potential facilitators identified for healthcare providers’ intimate partner violence screening.

CONCLUSION: Although higher-than-expected number of healthcare providers reported screening of pregnant women for intimate partner violence, the extent of screening is still suboptimal. The barrier to screening identified needs to be addressed and facilitators promoted. Receiving training among healthcare providers on intimate partner violence screening was associated with higher levels of screening; thus, this needs to be enhanced to optimize screening rates. Future studies should assess screening practices objectively and implement interventions to improve healthcare providers’ intimate partner violence screening rates.

IMPLICATIONS FOR THE PROFESSION AND/OR PATIENT CARE: Screening for intimate partner violence should be part of standard care provided by healthcare providers to all pregnant women during prenatal clinic visits. The study supports the need for more training for healthcare providers in aspects related to intimate partner violence screening in order to ensure prompt diagnosis and treatment of those affected, identify those at risk and increase awareness. There is a need to enhance healthcare providers’ capacity for intimate partner violence screening through education by integrating intimate partner violence screening pre- and post-registration courses and preparation programs or curriculum.

IMPACT: Intimate partner violence (IPV) in pregnancy is a global health problem. Screening for IPV by healthcare providers is suboptimal. This study found that only 56% of healthcare providers were routinely screening for IPV in Ugandan prenatal clinics. This study identified the main facilitators and one barrier to IPV screening.

REPORTING METHOD: This study has adhered to the relevant EQUATOR guidelines for quantitative studies.

PATIENT AND PUBLIC CONTRIBUTION: No patient was involved in this study.

PMID:38666414 | DOI:10.1111/jan.16198

Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2024 Apr 24. doi: 10.5507/bp.2024.013. Online ahead of print.

ABSTRACT

OBJECTIVE: Several factors are involved in the preservation of graft function after surgical myocardial revascularization. This follow-up study aimed to evaluate the effects of vein graft anastomosis and graft morphology on long-term graft patency a minimum of 10 years after aortocoronary bypass grafting. Setting and Cohorts. This was a sub-analysis of a study that enrolled patients after isolated bypass surgery at the University Hospital Ostrava in order to evaluate the long-term graft patency of the saphenous vein after endoscopic harvest, a minimum of 10 years after aortocoronary bypass grafting.

METHODS: Fifty angiograms, with a total of 90 grafts, after isolated myocardial revascularization were visualized using coronary computed tomography angiography, with 50% luminal stenosis or greater considered significant.

RESULTS: The overall graft patency rate was 72.3%. The differences in occlusion rates between sequential and individual grafts were not statistically significant (P=0.156). All y-grafts were totally occluded. Graft and target artery diameters had a statistically significant influence on patency (P=1.000 and 0.381, respectively). Longer graft length and higher calcium scores were associated with statistically significant graft occlusion (P=0.033 and 0.005, respectively).

CONCLUSION: Sequential grafts can be constructed safely, especially when the goal is complete myocardial revascularization.

PMID:38666413 | DOI:10.5507/bp.2024.013

Euro Surveill. 2024 Apr;29(17). doi: 10.2807/1560-7917.ES.2024.29.17.2300532.

ABSTRACT

BackgroundFollowing the 2022-2023 mpox outbreak, crucial knowledge gaps exist regarding orthopoxvirus-specific immunity in risk groups and its impact on future outbreaks.AimWe combined cross-sectional seroprevalence studies in two cities in the Netherlands with mathematical modelling to evaluate scenarios of future mpox outbreaks among men who have sex with men (MSM).MethodsSerum samples were obtained from 1,065 MSM attending Centres for Sexual Health (CSH) in Rotterdam or Amsterdam following the peak of the Dutch mpox outbreak and the introduction of vaccination. For MSM visiting the Rotterdam CSH, sera were linked to epidemiological and vaccination data. An in-house developed ELISA was used to detect vaccinia virus (VACV)-specific IgG. These observations were combined with published data on serial interval and vaccine effectiveness to inform a stochastic transmission model that estimates the risk of future mpox outbreaks.ResultsThe seroprevalence of VACV-specific antibodies was 45.4% and 47.1% in Rotterdam and Amsterdam, respectively. Transmission modelling showed that the impact of risk group vaccination on the original outbreak was likely small. However, assuming different scenarios, the number of mpox cases in a future outbreak would be markedly reduced because of vaccination. Simultaneously, the current level of immunity alone may not prevent future outbreaks. Maintaining a short time-to-diagnosis is a key component of any strategy to prevent new outbreaks.ConclusionOur findings indicate a reduced likelihood of large future mpox outbreaks among MSM in the Netherlands under current conditions, but emphasise the importance of maintaining population immunity, diagnostic capacities and disease awareness.

PMID:38666400 | DOI:10.2807/1560-7917.ES.2024.29.17.2300532

Neuropsychol Rehabil. 2024 Apr 26:1-25. doi: 10.1080/09602011.2024.2343155. Online ahead of print.

ABSTRACT

ABSTRACTTo assess the impact of ankle-foot orthoses (AFOs) on mobility and gait during dual-task walking in post-stroke survivors. In this cross-sectional, factorial design trial, stroke survivors performed four randomized tasks: (1) dual-task walking with AFOs, (2) single-task walking with AFOs, (3) dual-task walking without AFOs, and (4) single-task walking without AFOs. Primary outcome was the Timed Up and Go (TUG) test, with secondary outcomes including gait metrics, Tinetti scores, and auditory N-back tests. In the results, 48 subjects (38 males and 10 females; 19-65 years) completed the trial. Patients had a greater TUG score with AFOs compared with non-AFOs conditions (95% CI: 7.22-14.41, P < 0.001) in single-task and dual-task conditions. Secondary outcomes showed marked enhancement with AFOs during dual-task walking, with significant interaction effects in gait metrics, balance, and cognitive function (P < 0.05). Although not statistically significant, dual-task effects of TUG and walking speed were more pronounced during dual-task walking. In conclusion, AFOs enhance mobility and gait during both single and dual-task walking in post-stroke survivors.

PMID:38666380 | DOI:10.1080/09602011.2024.2343155

J Periodontal Res. 2024 Apr 26. doi: 10.1111/jre.13279. Online ahead of print.

ABSTRACT

AIM: This study evaluated the efficacy of quadrantwise subgingival instrumentation (Q-SI) versus one-stage full-mouth subgingival instrumentation (FM-SI) on probing depth and periodontal pathogen reduction over a 6-month follow-up period, as well as whether baseline periodontal pathogens influenced the impact of periodontal treatment protocols on outcomes.

METHODS: Patients with periodontitis were randomized to receive Q-SI (n = 43) or FM-SI (n = 45). Patients were instructed and motivated to maintain optimal oral hygiene during the treatment sessions. Clinical (probing pocket depth [PPD], clinical attachment loss [CAL], and bleeding on probing [BOP]) and periodontal pathogens were assessed at baseline and after 30, 90, and 180 days. Total bacterial load and periodontal pathogens were analysed via real-time PCR.

RESULTS: At the 6-month follow-up, the median PPD decreased from 4.8 mm (interquartile range [IQR]: 4.3-5.2) to 2.6 mm (IQR: 2.3-2.9) in FM-SI patients and from 4.7 mm (IQR: 4.1-5.2) to 3.2 mm (IQR: 2.4-3.5) in Q-SI patients (p < .001). At 6 months, FM-SI was more effective at reducing the median proportions of Porphyromonas gingivalis (Pg), Aggregatibacter actinocomyctemcomitans, and Tannerella forsythia (Tf) (p < .001 for each value). Multilevel linear regression analysis demonstrated that high baseline PPD (p = .029), Pg (p = .014), and Tf (p < .001) levels and the FM-SI protocol (p < .001) were statistically significant predictors of PPD reduction at 6 months. Furthermore, PPD reduction was significantly greater in the FM-SI group when lower baseline Pg levels were detected.

CONCLUSION: The FM-SI was more effective than the Q-SI in reducing the mean PPD and number of periodontal pathogens in periodontitis patients over a 6-month follow-up period. Higher baseline PPD and Pg levels had a negative impact on PPD reduction at 6 months after FM-SI.

PMID:38666373 | DOI:10.1111/jre.13279

Eur Heart J. 2024 Apr 26:ehae132. doi: 10.1093/eurheartj/ehae132. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Longitudinal change in income is crucial in explaining cardiovascular health inequalities. However, there is limited evidence for cardiovascular disease (CVD) risk associated with income dynamics over time among individuals with type 2 diabetes (T2D).

METHODS: Using a nationally representative sample from the Korean National Health Insurance Service database, 1 528 108 adults aged 30-64 with T2D and no history of CVD were included from 2009 to 2012 (mean follow-up of 7.3 years). Using monthly health insurance premium information, income levels were assessed annually for the baseline year and the four preceding years. Income variability was defined as the intraindividual standard deviation of the percent change in income over 5 years. The primary outcome was a composite event of incident fatal and nonfatal CVD (myocardial infarction, heart failure, and stroke) using insurance claims. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated after adjusting for potential confounders.

RESULTS: High-income variability was associated with increased CVD risk (HRhighest vs. lowest quartile 1.25, 95% CI 1.22-1.27; Ptrend < .001). Individuals who experienced an income decline (4 years ago vs. baseline) had increased CVD risk, which was particularly notable when the income decreased to the lowest level (i.e. Medical Aid beneficiaries), regardless of their initial income status. Sustained low income (i.e. lowest income quartile) over 5 years was associated with increased CVD risk (HRn = 5 years vs. n = 0 years 1.38, 95% CI 1.35-1.41; Ptrend < .0001), whereas sustained high income (i.e. highest income quartile) was associated with decreased CVD risk (HRn = 5 years vs. n = 0 years 0.71, 95% CI 0.70-0.72; Ptrend < .0001). Sensitivity analyses, exploring potential mediators, such as lifestyle-related factors and obesity, supported the main results.

CONCLUSIONS: Higher income variability, income declines, and sustained low income were associated with increased CVD risk. Our findings highlight the need to better understand the mechanisms by which income dynamics impact CVD risk among individuals with T2D.

PMID:38666368 | DOI:10.1093/eurheartj/ehae132

Influenza Other Respir Viruses. 2024 May;18(5):e13300. doi: 10.1111/irv.13300.

ABSTRACT

BACKGROUND: Identifying children at risk for severe COVID-19 disease from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may guide future mitigation interventions. Using sentinel surveillance data, we aimed to identify risk factors for SARS-CoV-2-associated hospitalisation among patients aged ≤ 18 years with respiratory illness.

METHODS: From April 2020 to March 2022, patients meeting study case definitions were enrolled at four outpatient influenza-like illness (ILI) and five inpatient severe respiratory infection (SRI) surveillance sites and tested for SARS-CoV-2 infection using polymerase chain reaction (PCR). Each ILI clinic shared a catchment area with its corresponding SRI hospital. Potential risk factors for SARS-CoV-2-associated hospitalisation were analysed using multivariable logistic regression by comparing inpatient versus outpatient SARS-CoV-2 cases.

RESULTS: Of 4688 participants aged ≤ 18 years, 4556 (97%) with complete PCR and HIV data were included in the analysis. Among patients with ILI and SRI, 92/1145 (8%) and 154/3411 (5%) tested SARS-CoV-2 positive, respectively. Compared to outpatients, hospitalised SARS-CoV-2 cases were associated with age < 6 months ([adjusted odds ratio (aOR) 8.0, 95% confidence interval (CI) 2.7-24.0] versus 1-4 years); underlying medical condition other than HIV [aOR 5.8, 95% CI 2.3-14.6]; laboratory-confirmed Omicron BA.1/BA.2 or Delta variant ([aOR 4.9, 95% CI 1.7-14.2] or [aOR 2.8, 95% CI 1.1-7.3] compared to ancestral SARS-CoV-2); and respiratory syncytial virus coinfection [aOR 6.2, 95% CI 1.0-38.5].

CONCLUSION: Aligning with previous research, we identified age < 6 months or having an underlying condition as risk factors for SARS-CoV-2-associated SRI hospitalisation and demonstrated the potential of sentinel surveillance to monitor COVID-19 in children.

PMID:38666359 | DOI:10.1111/irv.13300