Tag: statistics

Ann Oper Res. 2024;342(3):1819-1835. doi: 10.1007/s10479-023-05491-3. Epub 2023 Jul 10.

ABSTRACT

Every day, hundreds of mosquito surveys are carried out around the world to inform policy and management decisions on how best to reduce or prevent the burden of mosquito-borne disease or mosquito nuisance. These surveys are usually time consuming and expensive. Mosquito surveillance is the essential component of vector management and control. However, surveillance is often carried out with a limited if not without a quantitative assessment of the sampling effort which can results in underpowered or overpowered studies, or certainly in overpowered studies when power analyses are carried out assuming independence in the measurements obtained from longitudinal and geographically proximal mosquito surveys. Many free, open-source and user-friendly tools to calculate statistical power are available, such as G*Power, glimmpse, powerandsamplesize.com website or R-cran packages (pwr and WebPower to name few of them). However, these tools may not be sufficient for powering mosquito surveys due to the additional properties of seasonal and spatially clustered repeated measurements required to reflect mosquito population dynamics. To facilitate power analysis for mosquito surveillance, we have developed TIMESS, a deployable browser-based Shiny app that estimates the number of repeated measurements and locations of mosquito surveys for a given effect size, power, significance level, seasonality and level of expected between-location clustering. In this article we describe TIMESS, its usage, strengths and limitations.

PMID:39606738 | PMC:PMC11588820 | DOI:10.1007/s10479-023-05491-3

ArXiv [Preprint]. 2024 Nov 19:arXiv:2411.12853v1.

ABSTRACT

Protein structures represent the key to deciphering biological functions. The more detailed form of similarity among these proteins is sometimes overlooked by the conventional structural comparison methods. In contrast, further advanced methods, such as Triangular Spatial Relationship (TSR), have been demonstrated to make finer differentiations. Still, the classical implementation of TSR does not provide for the integration of secondary structure information, which is important for a more detailed understanding of the folding pattern of a protein. To overcome these limitations, we developed the SSE-TSR approach. The proposed method integrates secondary structure elements (SSEs) into TSR-based protein representations. This allows an enriched representation of protein structures by considering 18 different combinations of helix, strand, and coil arrangements. Our results show that using SSEs improves the accuracy and reliability of protein classification to varying degrees. We worked with two large protein datasets of 9.2K and 7.8K samples, respectively. We applied the SSE-TSR approach and used a neural network model for classification. Interestingly, introducing SSEs improved performance statistics for Dataset 1, with accuracy moving from 96.0% to 98.3%. For Dataset 2, where the performance statistics were already good, further small improvements were found with the introduction of SSE, giving an accuracy of 99.5% compared to 99.4%. These results show that SSE integration can dramatically improve TSR key discrimination, with significant benefits in datasets with low initial accuracies and only incremental gains in those with high baseline performance. Thus, SSE-TSR is a powerful bioinformatics tool that improves protein classification and understanding of protein function and interaction.

PMID:39606719 | PMC:PMC11601798

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2024 Jun;2024:11226-11237. doi: 10.1109/cvpr52733.2024.01067. Epub 2024 Sep 16.

ABSTRACT

Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging, given the complexity of gigapixel slides. Traditionally, MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks, offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this, we propose Self-Interpretable MIL (SI-MIL), a method intrinsically designed for interpretability from the very outset. SI-MIL employs a deep MIL framework to guide an interpretable branch grounded on handcrafted pathological features, facilitating linear predictions. Beyond identifying salient regions, SI-MIL uniquely provides feature-level interpretations rooted in pathological insights for WSIs. Notably, SI-MIL, with its linear prediction constraints, challenges the prevalent myth of an inevitable trade-off between model interpretability and performance, demonstrating competitive results compared to state-of-the-art methods on WSI-level prediction tasks across three cancer types. In addition, we thoroughly benchmark the local-and global-interpretability of SI-MIL in terms of statistical analysis, a domain expert study, and desiderata of interpretability, namely, user-friendliness and faithfulness.

PMID:39606709 | PMC:PMC11601081 | DOI:10.1109/cvpr52733.2024.01067

Front Neurol. 2024 Nov 13;15:1479245. doi: 10.3389/fneur.2024.1479245. eCollection 2024.

ABSTRACT

BACKGROUND: According to recent research, there is a considerable correlation between the severity of coronary artery disease and the platelet-to-high-density lipoprotein cholesterol ratio (PHR), which suggests that PHR is a potentially valuable inflammatory biomarker. However, the body of current research offers insufficiently strong evidence to clarify the connection between PHR and the incidence of stroke. Therefore, this study aims to elucidate any potential associations between PHR and stroke risk.

METHODS: This study employed data from the China Health and Retirement Longitudinal Study (CHARLS) covering the period from 2011 to 2018. It included 5,872 participants who did not have a history of stroke in 2011. These patients were separated into four groups according to their baseline PHR quartiles. The main goal of the study was to focus on stroke outcomes. Stroke was defined as an occurrence of a cerebrovascular accident confirmed by a physician. We employed Cox proportional hazards regression models to investigate the association between PHR and the likelihood of experiencing a stroke. Furthermore, we conducted restricted cubic spline regression analysis and subgroup analysis.

RESULTS: The average follow-up period was 77.5 months, during which 390 participants experienced a stroke. In comparison to the lowest quartile group, participants in the highest quartile of PHR had a 49% increased risk of stroke (HR 1.49, 95% CI 1.13-1.96, p = 0.004). The adjusted multivariable Cox regression analysis maintained the statistical significance of this association (aHR 1.42, 95% CI 1.06-1.90, p = 0.019). After adjustment, a positive linear relationship between stroke risk and PHR was identified through restricted cubic spline regression analysis (nonlinear p > 0.05). Additionally, the impact of stroke was consistent across a variety of subgroups, as evidenced by subgroup analysis.

CONCLUSION: Our study indicates that higher PHR levels are significantly associated with an increased risk of stroke and that these levels can be used to identify groups that are at high risk of stroke.

PMID:39606701 | PMC:PMC11599229 | DOI:10.3389/fneur.2024.1479245

Front Pediatr. 2024 Nov 13;12:1407120. doi: 10.3389/fped.2024.1407120. eCollection 2024.

ABSTRACT

OBJECTIVE: To establish a predictive model for distinguishing testicular benign or yolk sac tumors in children.

METHODS: We retrospectively analyzed data for 119 consecutive patients with unilateral testicular tumors treated at a single institution from June 2014 to July 2020. The patients were divided into the benign (n = 90) and yolk sac (n = 29) tumor groups based on the pathological diagnosis. We recorded patient age, serum markers [serum alpha-fetoprotein (AFP), human chorionic gonadotropin], and tumor ultrasonic findings (maximum diameter, ultrasonic echo, blood flow signal). Predictive factors were identified using descriptive statistical methods. A nomogram was established for preoperative prediction. An additional 46 patients were used as a validation cohort to verify the model.

RESULTS: Patients with testicular yolk sac tumors were younger (median age: 14.0 vs. 34.0 months, P = 0.001) and had a higher incidence of elevated AFP levels (93.1% vs. 2.2%, P < 0.001). Ultrasonography indicated that testicular yolk sac tumors tended to have larger maximum diameters (26.5 ± 11.3 vs. 16.6 ± 9.2 cm, P < 0.001), a higher proportion of hypoechoic masses (44.8% vs. 8.9%, P < 0.001), and a higher incidence of masses with strong blood flow signals (93.1% vs. 5.6%, P < 0.001). A nomogram based on age, AFP levels, and ultrasound blood flow signals effectively predicted the probability of yolk sac tumor in children, with an accuracy of 0.98 (95% confidence interval: 0.984-1.003). The Brier score of the nomogram was 0.0002.

CONCLUSION: A nomogram based on age, AFP levels, and ultrasound blood flow signals can effectively predict the probability of testicular yolk sac tumor preoperatively, aiding in clinical decision-making and patient counseling.

PMID:39606696 | PMC:PMC11598321 | DOI:10.3389/fped.2024.1407120

EClinicalMedicine. 2024 Nov 12;78:102932. doi: 10.1016/j.eclinm.2024.102932. eCollection 2024 Dec.

ABSTRACT

BACKGROUND: The Consolidated Standards of Reporting Trials (CONSORT) statement has improved the quality of reporting of randomised trials. Extensions to the CONSORT statement are often needed to address specific issues of trial reporting, including those relevant to particular types of interventions. Methodological and reporting deficiencies in clinical trials of implantable neurostimulation devices are common. The CONSORT-iNeurostim extension is a new reporting guideline for randomised controlled trials evaluating implantable neurostimulation devices.

METHODS: CONSORT-iNeurostim was developed using the EQUATOR methodological framework including a literature review and expert consultation to generate an initial list of candidate items. The candidate items were included in a two-round Delphi survey, discussed at an international consensus meeting (42 stakeholders including healthcare professionals, methodologists, journal editors and industry representatives from the United States, United Kingdom, Netherlands and other countries), and refined through a checklist pilot (18 stakeholders).

FINDINGS: The initial extension item list included 49 candidate items relevant to CONSORT-iNeurostim. We received 132 responses in the first round of the Delphi survey and 99 responses in the second round. Participants suggested an additional 20 candidate items for CONSORT-iNeurostim during the first round of the survey, and those achieving initial consensus were discussed at the consensus meeting. The CONSORT-iNeurostim extension includes 7 new checklist items, including one item for reporting the neurostimulation intervention comprising a separate checklist of 14 items.

INTERPRETATION: The CONSORT-iNeurostim extension will promote increased transparency, clarity, and completeness of trial reports of implantable neurostimulation devices. It will assist journal editors, peer-reviewers, and readers to better interpret the appropriateness and generalisability of the methods used and reported outcomes.

FUNDING: Abbott, Boston Scientific Corp., Mainstay Medical, Medtronic Ltd, Nevro Corp. and Saluda Medical.

PMID:39606687 | PMC:PMC11600657 | DOI:10.1016/j.eclinm.2024.102932

Avicenna J Med Biotechnol. 2024 Oct-Dec;16(4):260-267. doi: 10.18502/ajmb.v16i4.16742.

ABSTRACT

BACKGROUND: Simulated Physiological Oocyte Maturation (SPOM) mimics in vitro the physiological events of oocyte maturation in the presence of cAMP modulators. These modulators increase the intracellular concentrations of cAMP, which inhibits the immediate resumption of meiosis and gives the oocyte more time to gain optimal developmental competence. In addition, L-carnitine helps to increase the energy supply of cells through the β-oxidation of fatty acids. This study aimed to investigate the effect of SPOM and L-carnitine supplementation during In Vitro Maturation (IVM) and In Vitro Culture (IVC) on the developmental competence of bovine oocytes.

METHODS: Ovarian Cumulus Complexes (COCs) were cultured in the presence or absence of forskolin+IBMX during the first 2 hr of IVM (pre-IVM) with or without L-carnitine (LC) during IVM or IVC in six experimental groups as follows: I) pre-IVM (pre-IVM group), II) pre-IVM with L-carnitine supplementation during IVM (pre-IVM/LC group), III) L-carnitine supplementation during IVM (IVM/LC group), IV) L-carnitine supplementation during in vitro culture (IVC/LC group), V) pre-IVM+ IVC/LC group, and VI) no treatment during IVM and IVC (Control group). The cleavage and blastocyst rates, the blastocysts’ total cells number, and the expression of Nanog, Bax, Oct4, Cdx2, and Ifnt genes in resulting blastocysts were assessed. To assess differences among experimental groups, a one-way analysis of variance was initially employed, followed by post hoc Fisher LSD. The difference between groups was considered statistically significant when p<0.05.

RESULTS: The cleavage and blastocyst rates in the Pre-IVM and Pre-IVM/LC groups was higher than control group and other groups (p≤0.05) except for IVC/LC and IVM/LC groups, respectively. The number of blastocyst’s Inner Cell Mass (ICM) in pre-IVM and Pre-IVM/LC groups as well as the ratio of ICM/TE were higher than control group (p<0.05). The expression of OCT4, CDX2, and IFNT increased in both the pre-IVM and pre-IVM/LC groups compared to the control group (p<0.05).

CONCLUSION: In conclusion, the application of SPOM-adapted IVM and L-carnitine during IVM of bovine oocyte improves the quantity and quality of the resulting embryos.

PMID:39606683 | PMC:PMC11589426 | DOI:10.18502/ajmb.v16i4.16742

Front Med (Lausanne). 2024 Nov 13;11:1401685. doi: 10.3389/fmed.2024.1401685. eCollection 2024.

ABSTRACT

INTRODUCTION: Leprosy is a chronic infectious disease caused by the agent Mycobacterium leprae, characterized by its high disabling power. Data points to Brazil being the second country with the highest number of cases in the world, behind only India, representing a major challenge for public health. This work aims to determine the prevalence of paucibacillary (PB) cases in relation to leprosy cases in Brazil, using data published in the literature.

METHODS: This is a systematic review and meta-analysis carried out with studies from the last 20 years, being developed based on the Preferred Reporting Items for Systematic Review and Meta-analyzes (PRISMA).The search was carried out in the databases: PUBMED, SciELO, LILACS (via VHL)and Science Direct in October 2023, using the following descriptors (((“Brazil” [Mesh]) AND (“Leprosy, paucibacillary” [Mesh])) AND “Epidemiology” [Mesh]), in English, Portuguese and Spanish. Original studies of the analytical case-control, cohort, cross-sectional, epidemiological types were selected, as well as articles with satisfactory information for numerical extraction with separate data on the paucibacillary and multibacillary clinical forms. The methodological quality assessment followed the JBI critical appraisal checklist. Statistical analysis was performed using the Comprehensive Meta-Analyses-CMA software, version 3.0 (Biostat, Engewood, NJ, United States).

RESULTS: The meta-analysis of the 48 studies obtained a paucibacillary prevalence rate in Brazil of 50.5% or 0.505 (95% CI = 0.502-0.509).The differences in the analyzes were statistically significant (Q-value 4302.681;df 47; I 98.905), with a high heterogeneity value evidenced by I² (98.905). This analysis demonstrated that the frequency in the Midwest region was the highest and the South region was the lowest (21.4%). Begg’s (Kendall Tau p = 0.35) and Egger’s tests (p = 0.20) were performed, in which no high publication bias was noted. Subgroup analysis indicated that paucibacillary cases varied from region to region, with the Midwest region having the highest prevalence and the South region having the lowest.

CONCLUSION: The results stand out significantly for the research gaps that investigate PB cases, requiring more research aimed at investigating the paucibacillary clinical form that can contribute to the early diagnosis of leprosy.

SYSTEMATIC REVIEW REGISTRATION: PROSPERO code: CRD42024514106.

PMID:39606626 | PMC:PMC11600445 | DOI:10.3389/fmed.2024.1401685

Wellcome Open Res. 2024 Sep 17;9:526. doi: 10.12688/wellcomeopenres.22699.1. eCollection 2024.

ABSTRACT

BACKGROUND: Hypertension affects over one billion people worldwide, posing a significant global health burden. Clinical practice guidelines could play a key role in guiding healthcare providers in improving hypertension management. However, how the quality of hypertension CPGs differs across country income settings is not well understood. This study aims to explore variation in the quality of hypertension CPGs, comparing low-, middle-, and high-income countries, using the Appraisal of Guidelines for Research and Evaluation (AGREE) II tool.

METHODS: A Medline and grey literature search was conducted to identify hypertension CPGs in English from every country from January 2012 to September 2022. Two reviewers independently assessed and scored each CPG against the AGREE II tool. Results were described and the Kruskal-Wallis test was used to test for statistically significant difference in the domain scores across country income groups.

RESULTS: Forty-three CPGs were included for analysis from across income settings. Guidelines from HICs scored higher in four out of the six domains. The highest scoring domain was 4: “clarity and presentation” (median score 83%), the lowest scoring was domain 6 “editorial independence” (median score 0%). Statistically significant differences between income settings were observed for domain 3 “rigour of development” (p <0.001), domain 4 “clarity and presentation” (p = 0.03) and domain 6 “editorial independence” (p = 0.04).

CONCLUSIONS: Whilst some variation exists in guideline quality across country income levels, the greatest degree of variation exists across the domains of the AGREE II tool. Global efforts to improve the quality of hypertension guidelines should focus on the transparent statement of editorial independence of guideline committees and apply rigorous replicable methods in the authoring of guidelines. Establishing national and international communities of practice to collaborate across income settings may reduce duplication of resource, allow for shared learning and promote the development of high-quality hypertension CPGs.

PMID:39606620 | PMC:PMC11599801 | DOI:10.12688/wellcomeopenres.22699.1

J Inherit Metab Dis. 2024 Nov 27. doi: 10.1002/jimd.12823. Online ahead of print.

ABSTRACT

Alterations in brain structure are frequently observed in adults with early-treated phenylketonuria (PKU) compared to healthy controls, with cerebral white matter (WM) being particularly affected. The extent to which temporary elevation of phenylalanine (Phe) levels impacts WM remains unclear. We conducted a double-blind, randomised, placebo-controlled crossover trial to investigate the effects of a 4-week high Phe exposure on cerebral WM and its relationship to cognitive performance and metabolic parameters in adults with PKU. In this study, 27 adults with early-treated classical PKU (aged 19-48 years) underwent diffusion tensor imaging (DTI) before and after the 4-week Phe and placebo interventions. Fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were analysed using tract-based spatial statistics. Neuropsychological examinations at each timepoint evaluated executive functions and attention. Additionally, brain Phe levels were measured using MR spectroscopy, and blood levels of Phe, tyrosine, and tryptophan were assessed after an overnight fast. Following the Phe period, significant decreases in AD, MD, and RD were observed compared to the placebo period, particularly in the posterior corona radiata and optic radiation. Notably, these WM changes were reversible in patients who first received Phe (n = 13). Cognitive performance and metabolic parameters were not significantly related to DTI scalars after the Phe period. In conlcusion, a 4-week Phe elevation induced reversible microstructural alterations in cerebral WM. Further investigation is necessary to determine the clinical implication of these changes.

PMID:39604093 | DOI:10.1002/jimd.12823