Tag: statistics

Oncologist. 2022 Feb 3;27(1):48-56. doi: 10.1093/oncolo/oyab001.

ABSTRACT

OBJECTIVES: The eighth edition American Joint Committee on Cancer (AJCC) Staging incorporates significant changes to the seventh edition in the staging of oropharyngeal squamous cell carcinomas (OPSCC). An important change was the inclusion of OPSCC associated with the human papilloma virus (HPV). Our goal is to compare the performance of both staging systems for patients with HPV-selected and unselected clinical characteristics for OPSCC.

METHODS: Using the Surveillance, Epidemiology, and End Results (SEER) database, 2004-2016, we identified patients with likely HPV-associated OPSCC based on surrogate markers (white males aged <65 years old with squamous cell carcinomas of the tonsil and base of tongue), excluding those who underwent surgery. We re-classified these patients using seventh and eighth edition staging for HPV-selected OPSCC and compared the prediction performance of both staging editions for overall survival (OS) and disease-specific survival (DSS). We performed the same analysis for clinically unselected patients with OPSCC.

RESULTS: Our analysis included 9554 patients with a median follow-up of 67 months. Comparing the eighth versus seventh edition for our HPV-selected cohort, clinical staging changed for 92.3% of patients and 10-year OS was 62.2%, 61.2%, 35.3%, and 15.5% for Stage I, II, III, and IV, versus 52.9%, 59.2%, 61.6%, 55.1%, 38.3%, and 15.5% for stage I, II, III, IVA, IVB, and IVC, respectively. A similar pattern was observed for 10-year DSS. The concordance statistics for our HPV-selected cohort were improved for both AJCC 7 (0.6260) and AJCC 8 (0.6846) compared with the unselected cohort, 0.5860 and 0.6457 for AJCC 7 and 8, respectively.

CONCLUSION: The overall performance of discrimination improved from AJCC 7 to AJCC 8 for both clinically selected and unselected patients, but more notably for our HPV-selected cohort. Despite the lack of statistically significant differentiation between Stages I and II in AJCC 8 in either groups, markedly improved discrimination was observed between Stages I/II, III, and IV in the HPV-selected cohort.

PMID:35305095 | DOI:10.1093/oncolo/oyab001

J Med Entomol. 2022 Mar 19:tjac005. doi: 10.1093/jme/tjac005. Online ahead of print.

ABSTRACT

Dengue Hemorrhagic Fever (DHF) is a major mosquito-borne viral disease. Studies have reported a strong correlation between weather, the abundance of Aedes aegypti, the vector of DHF virus, and dengue incidence. However, this conclusion has been based on the general climate pattern of wide regions. In general, however, the human population, level of infrastructure, and land-use change in rural and urban areas often produce localized climate patterns that may influence the interaction between climate, vector abundance, and dengue incidence. Thoroughly understanding this correlation will allow the development of a customized and precise local early warning system. To achieve this purpose, we conducted a cohort study, during January-December 2017, in 16 districts in Bandung, West Java, Indonesia. In the selected areas, local weather stations and modified light mosquito traps were set up to obtain data regarding daily weather and the abundance of adult female Ae. aegypti. A generalized linear model was applied to analyze the effect of local weather and female adult Ae. aegypti on the number of dengue cases. The result showed a significant non-linear correlation among mosquito abundance, maximum temperature, and dengue cases. Using our model, the data showed that the addition of a single adult Ae. aegypti mosquito increased the risk of dengue infection by 1.8%, while increasing the maximum temperature by one degree decreased the risk by 17%. This finding suggests specific actionable insights needed to supplement existing mosquito eradication programs.

PMID:35305089 | DOI:10.1093/jme/tjac005

Hum Brain Mapp. 2022 Mar 19. doi: 10.1002/hbm.25829. Online ahead of print.

ABSTRACT

The reproducibility crisis in neuroimaging has led to an increased demand for standardized data processing workflows. Within the ENIGMA consortium, we developed HALFpipe (Harmonized Analysis of Functional MRI pipeline), an open-source, containerized, user-friendly tool that facilitates reproducible analysis of task-based and resting-state fMRI data through uniform application of preprocessing, quality assessment, single-subject feature extraction, and group-level statistics. It provides state-of-the-art preprocessing using fMRIPrep without the requirement for input data in Brain Imaging Data Structure (BIDS) format. HALFpipe extends the functionality of fMRIPrep with additional preprocessing steps, which include spatial smoothing, grand mean scaling, temporal filtering, and confound regression. HALFpipe generates an interactive quality assessment (QA) webpage to rate the quality of key preprocessing outputs and raw data in general. HALFpipe features myriad post-processing functions at the individual subject level, including calculation of task-based activation, seed-based connectivity, network-template (or dual) regression, atlas-based functional connectivity matrices, regional homogeneity (ReHo), and fractional amplitude of low-frequency fluctuations (fALFF), offering support to evaluate a combinatorial number of features or preprocessing settings in one run. Finally, flexible factorial models can be defined for mixed-effects regression analysis at the group level, including multiple comparison correction. Here, we introduce the theoretical framework in which HALFpipe was developed, and present an overview of the main functions of the pipeline. HALFpipe offers the scientific community a major advance toward addressing the reproducibility crisis in neuroimaging, providing a workflow that encompasses preprocessing, post-processing, and QA of fMRI data, while broadening core principles of data analysis for producing reproducible results. Instructions and code can be found at https://github.com/HALFpipe/HALFpipe.

PMID:35305030 | DOI:10.1002/hbm.25829

Liver Int. 2022 Mar 18. doi: 10.1111/liv.15223. Online ahead of print.

ABSTRACT

BACKGROUND & AIM: Liver transplantation (LT) selection models for hepatocellular carcinoma (HCC) have not been proposed to predict waitlist dropout due to tumor progression. The aim of this study was to compare the alfa-fetoprotein (AFP) model and other pre-LT models in their prediction of HCC dropout.

METHODS: A multicenter cohort study was conducted in 20 Latin American transplant centers, including 994 listed patients for LT with HCC from 2012 to 2018. Longitudinal tumor characteristics, and patterns of progression were recorded at time of listing, after treatments and at last follow-up over the waitlist period. Competing risk regression models were performed, and model’s discrimination was compared estimating Harrell’s adapted c-statistics.

RESULTS: HCC dropout rate was significantly higher in patients beyond [24% (95% CI 16-28)] compared to those within Milan criteria [8% (95% IC 5-12%); P<.0001], with a SHR of 3.01 (95% CI 2.03-4.47)], adjusted for waiting list time and bridging therapies (c-index 0.63 (95% CI 0.57;0.69). HCC dropout rates were higher in patients with AFP scores >2 [adjusted SHR of 3.17 (CI 2.13-4.71)], c-index of 0.71 (95% CI 0.65-0.77; P=0.09 vs Milan). Similar discrimination power for HCC dropout was observed between the AFP score and the Metroticket 2.0 model. In patients within Milan, an AFP score >2 points discriminated two populations with a higher risk of HCC dropout [SHR 1.68 (95% CI 1.08-2.61)].

CONCLUSIONS: Pre-transplant selection models similarly predicted HCC dropout. However, the AFP model can discriminate a higher risk of dropout among patients within Milan criteria.

PMID:35304813 | DOI:10.1111/liv.15223

Cancer Med. 2022 Mar 18. doi: 10.1002/cam4.4679. Online ahead of print.

ABSTRACT

BACKGROUND: Immune checkpoint inhibitor/tyrosine kinase inhibitor (ICI/TKI) combinations are a new standard of care for the initial treatment of metastatic renal cell carcinoma (mRCC). Their efficacy and toxicity beyond the first-line setting remain poorly defined.

METHODS: We retrospectively reviewed charts for 85 adults with mRCC of any histology receiving combination of ICI/TKI in any line of treatment at two academic centers as of 05/01/2020. We collected clinical, pathological, and treatment-related variables. Outcomes including objective response rate (ORR), progression-free survival (PFS), and toxicity were analyzed via descriptive statistics and the Kaplan-Meier method.

RESULTS: Patients received pembrolizumab, nivolumab, avelumab, or nivolumab-ipilimumab, with concurrent use of sunitinib, axitinib, pazopanib, lenvatinib, or cabozantinib. Thirty-three patients received first-line ICI/TKI therapy, while 52 received ≥ second-line ICI/TKI. The efficacy of ICI/TKI therapy decreased with increasing lines of treatment (ORR: 56.7%, 37.5%, 21.4%, and 21%; median PFS [mPFS]: 15.2, 14.2, 10.1, and 6.8 months, for first, second, third, and ≥ fourth line therapy, respectively). In the ≥ second-line setting, ICI/TKI was most useful in patients who received ICI only, with an ORR of 50% and a mPFS of 9.1 months. Efficacy was limited in patients who received both TKI and ICI previously, with an ORR of 20% and a mPFS of 5.5 months. Overall, ≥ second-line ICI/TKI was tolerable with 25 of 52 (52%) patients developing grade ≥3 adverse events.

CONCLUSIONS: ICI/TKI combination therapy is feasible and safe beyond the first-line setting. Prior treatment history appears to impact efficacy but has a lesser effect on safety/tolerability.

PMID:35304832 | DOI:10.1002/cam4.4679

J Prosthodont. 2022 Mar 18. doi: 10.1111/jopr.13506. Online ahead of print.

ABSTRACT

PURPOSE: The annealing and firing cycle’s effect on the adaptation of cobalt-chromium (CoCr) restorations fabricated by additive manufacturing has been poorly documented. This study compared the marginal and internal fit of CoCr three-unit fixed dental prostheses before and after firing cycles.

MATERIAL AND METHODS: The first right maxillary premolar (MP) and molar (MM) on a typodont model, were prepared with a circumferential 1.2 mm chamfer, 2 mm occlusal reduction, and total taper of 8 degrees, to receive 3-unit fixed dental prostheses (FDP). After the framework design, 20 framework specimens were fabricated using CoCr metal powder by selective laser melting. The replica technique was used for marginal and internal fit measurements in mesiodistal and buccolingual planes. The specimens were submitted to an annealing process, and to ceramic firing protocol. Measurements were repeated after each firing cycle. The data were compared by using Levene test, t-test, and analysis of variance (ANOVA) (α = .05).

RESULTS: A significant difference was found in the total intaglio surface discrepancy between the 3 treatments. The annealing treatment induced a statistical difference in the discrepancy value compared to the as printed state (P = .028). A significant difference was detected between the initial manufacturing phase and the ceramic layering firing cycle (P = .003).

CONCLUSIONS: Firing cycles induced an alteration of the frameworks adaptation. This article is protected by copyright. All rights reserved.

PMID:35304798 | DOI:10.1111/jopr.13506

J Evol Biol. 2022 Mar 18. doi: 10.1111/jeb.13998. Online ahead of print.

ABSTRACT

Assortative mating occurs when paired individuals of the same population are more similar than expected by chance. This form of non-random assortment has long been predicted to play a role in many evolutionary processes because assortatively mated individuals are assumed to be genetically similar. However, this assumption may always hold for labile traits, or traits that are measured with error. For such traits, there is a variety of proximate mechanisms that can drive phenotypic resemblance between mated partners that, notably, have very different evolutionary repercussions. Bettering our understanding of the role of assortative mating in evolution will thus require insight into its proximate causes. To date, empirical research remains sparse, especially when for labile traits. This special issue aims to stimulate such research while promoting the usage and development of statistical approaches allowing the quantification of the relative roles of alternative proximate mechanisms causing assortative mating. To this end, we first describe how the phenotypic covariance between mated partners can be usefully partitioned into components that capture one or several of five distinct mechanisms. We then demonstrate why the importance of mechanisms causing genetic covariance between the traits of partners may often be overestimated. Finally, we detail how the evolutionary causes and consequences of the diverse mechanisms may be identified.

PMID:35304800 | DOI:10.1111/jeb.13998

J Clin Pharm Ther. 2022 Mar 18. doi: 10.1111/jcpt.13641. Online ahead of print.

ABSTRACT

WHAT IS KNOWN AND OBJECTIVE: Premature birth affects more than 15 million infants, as well as mothers and families around the world. With the relaxation of the two-child policy, the problem of premature birth has become relatively prominent in China. According to statistics, China had a birth population of 15.23 million in 2018, with a considerably large number of premature births. This study aims to evaluate the efficacy and safety of tocolysis in the treatment of preterm delivery, provide clinical evidence for medical staff and promote the self-management of patients with premature births.

METHODS: Four English databases (PubMed, Embase, Cochrane Library and Web of Science) were retrieved by computer, the retrieval time was from the establishment of each database to November 2021, and the randomized controlled trials for the treatment of preterm delivery were screened according to the pre-set natriuretic exclusion criteria. After literature screening, data selection and risk of bias evaluation were independently conducted by two researchers. R 4.1.1 and Stata 17.0 software were used for statistical analysis.

RESULTS AND DISCUSSION: A total of 44 RCTs were included, including 6939 patients. The results of network meta-analysis reveal that in terms of effectiveness, indomethacin was the most effective intervention measure, followed by nifedipine, and the difference was statistically significant; regarding safety, nifedipine was the safest intervention measure, followed by indomethacin, and the difference was statistically significant; and in respect of adverse reactions, ritodrine had the highest probability, and the difference was statistically significant.

WHAT IS NEW AND CONCLUSION: Nifedipine may be better for delayed delivery and less likely to produce adverse pregnancy outcomes, followed by indomethacin. Limited by the number and quality of recipient studies, the aforementioned conclusions need to be verified through more high-quality studies. At the same time, the focus should be on patients with twin pregnancy and patients with clinical manifestations of extreme preterm delivery.

PMID:35304748 | DOI:10.1111/jcpt.13641

Ultraschall Med. 2022 Mar 18. doi: 10.1055/a-1778-3585. Online ahead of print.

ABSTRACT

AIM OF THE STUDY: The aim of the study is to examine the detection rates of malformations before and after the introduction of extended basic screening in Hesse by the Federal Joint Committee (Gemeinsamer Bundesausschuss, GQH) on July 1, 2013.

METHOD: This is a retrospective, mainly exploratory data analysis of quality assurance data from the Office for Quality Assurance in Hesse (GQH). The data was collected in the period from January 1, 2010 to December 31, 2016 in the obstetric departments of the Hessian hospitals using documentation forms. The classification and evaluation of the diagnoses is based on ICD-10-GM-2019.

RESULTS: At least one malformation is present in 0.7% of the cases. With a share of 30.0%, most of the congenital malformations are from the musculoskeletal system. 12.2% of the malformations come from the facial cleft, closely followed by malformations of the circulatory system with 11.3%. The highest prenatal detection rate (PDR) is found in congenital malformations of the nervous system at 56.8%. The lowest PDR is found in those of the genital organs with 2.1%. The PDR of cardiovascular malformations is 32.9%. Overall, a PDR of 25.2% is achieved. There was no change in the number of prenatal malformation diagnoses after the introduction of extended basic ultrasound. The distribution of malformation diagnoses not detected prenatally to the organ systems also has not changed after the introduction.

CONCLUSION: The introduction of extended basic ultrasound did not bring the desired improvement with regard to the PDR in Hesse. Alternative approaches should be considered.

PMID:35304733 | DOI:10.1055/a-1778-3585

Environ Sci Pollut Res Int. 2022 Mar 18. doi: 10.1007/s11356-022-19588-y. Online ahead of print.

ABSTRACT

Because of health concerns regarding the presence of enteric viruses in wastewater effluents, this study was designed to investigate the occurrence of human adenovirus (HAdV) in the irrigation water-soil-crop continuum. Viral particles were extracted from wastewater and wastewater- or water-irrigated soil and crop samples and analyzed using real-time PCR. Concentration of fecal indicator bacteria (FIB) were also determined. Quantitative microbial risk assessment was performed to determine the HAdV illness risk associated with the consumption of wastewater-irrigated vegetables. HAdV-F was detected in 74% of wastewater effluent samples with a mean concentration of 38 Genomic Copy (GC)/mL. HAdV was also detected in wastewater-irrigated soil (2 × 10² GC/g) and crop (< 10 GC/g) samples, with no statistically significant difference in concentrations between wastewater- and freshwater-irrigated samples. The results showed no correlation between concentrations of FIB and HAdV in the analyzed samples. Mean probability of illness risk from consumption of wastewater-irrigated vegetables was 4 × 10^-1 per person per year (pppy) which was about two orders of magnitude higher than the proposed value by WHO (10^-3 pppy) for safe reuse of wastewater. This finding suggests that the wastewater reuse for irrigation of vegetables eaten raw could pose a threat to human health with respect to the risk of viral illness, signifying stricter management of wastewater reuse. However, because of uncertainties in the QMRA model, particularly the ratio of infectious to non-infectious virus particles, more data is required to validate the predicted risk. This information is especially important in arid and semi-arid regions where high temperatures, UV radiation intensity, and desiccation can efficiently inactivate microorganisms in the environment.

PMID:35304720 | DOI:10.1007/s11356-022-19588-y