Tag: statistics

J Clin Lab Anal. 2022 Jul 19:e24606. doi: 10.1002/jcla.24606. Online ahead of print.

ABSTRACT

BACKGROUND: Several studies have interrogated the molecular pathways and their interacting genes underlying bladder cancer (BCa) tumorigenesis, yet, the role of homeobox genes is still poorly understood. Specifically, HOXA13, which plays an important role as a major actor in the urogenital tract’s development.

METHODS: Immunohistochemical (IHC) staining was performed to inspect the differential expression of HOXA13 protein in non-muscle-invasive bladder cancer (NMIBC) and non-tumoral tissues. A semiquantitative scoring system was adopted to evaluate the IHC labeling. Correlation to clinical parameters was performed by descriptive statistics. Overall survival was estimated by the Kaplan-Meier method and Cox regression model. The functional HOX A13 protein association networks (PPI) were obtained using String 11.0 database.

RESULTS: HOX A13 exhibited cytoplasmic and nuclear staining. Its expression levels were lower in high-grade NMIBC (HG NMIBC) compared to low-grade ones (LG NMIBC). The expression of HOX A13 was correlated to tumor grade (LG/HG) (p = 0.036) and stage (TA/T1) (p = 0.036). Nevertheless, its expression was not correlated to clinical parameters and was not able to predict the overall survival of patients with HG NMIBC. Finally, PPI analysis revealed that HOX A13 seems to be a part of a molecular network holding mainly PBX1, MEIS, ALDH1A2, HOX A10, and HOX A11.

CONCLUSION: The deregulation of HOX A13 is not associated with the prognosis of BCa. It seems to be rather implicated in the early initiation of urothelial tumorigenesis and thus may serve as a diagnostic marker in patients with NMIBC. Further experimentations on larger validation sets are mandatory.

PMID:35853090 | DOI:10.1002/jcla.24606

PLoS One. 2022 Jul 19;17(7):e0270872. doi: 10.1371/journal.pone.0270872. eCollection 2022.

ABSTRACT

In this article, we present a methodology which takes as input a collection of retracted articles, gathers the entities citing them, characterizes such entities according to multiple dimensions (disciplines, year of publication, sentiment, etc.), and applies a quantitative and qualitative analysis on the collected values. The methodology is composed of four phases: (1) identifying, retrieving, and extracting basic metadata of the entities which have cited a retracted article, (2) extracting and labeling additional features based on the textual content of the citing entities, (3) building a descriptive statistical summary based on the collected data, and finally (4) running a topic modeling analysis. The goal of the methodology is to generate data and visualizations that help understanding possible behaviors related to retraction cases. We present the methodology in a structured step-by-step form following its four phases, discuss its limits and possible workarounds, and list the planned future improvements.

PMID:35853087 | DOI:10.1371/journal.pone.0270872

PLoS Genet. 2022 Jul 19;18(7):e1010299. doi: 10.1371/journal.pgen.1010299. Online ahead of print.

ABSTRACT

In recent work, Wang et al introduced the “Sum of Single Effects” (SuSiE) model, and showed that it provides a simple and efficient approach to fine-mapping genetic variants from individual-level data. Here we present new methods for fitting the SuSiE model to summary data, for example to single-SNP z-scores from an association study and linkage disequilibrium (LD) values estimated from a suitable reference panel. To develop these new methods, we first describe a simple, generic strategy for extending any individual-level data method to deal with summary data. The key idea is to replace the usual regression likelihood with an analogous likelihood based on summary data. We show that existing fine-mapping methods such as FINEMAP and CAVIAR also (implicitly) use this strategy, but in different ways, and so this provides a common framework for understanding different methods for fine-mapping. We investigate other common practical issues in fine-mapping with summary data, including problems caused by inconsistencies between the z-scores and LD estimates, and we develop diagnostics to identify these inconsistencies. We also present a new refinement procedure that improves model fits in some data sets, and hence improves overall reliability of the SuSiE fine-mapping results. Detailed evaluations of fine-mapping methods in a range of simulated data sets show that SuSiE applied to summary data is competitive, in both speed and accuracy, with the best available fine-mapping methods for summary data.

PMID:35853082 | DOI:10.1371/journal.pgen.1010299

IEEE Trans Neural Netw Learn Syst. 2022 Jul 19;PP. doi: 10.1109/TNNLS.2022.3190509. Online ahead of print.

ABSTRACT

Multiarmed Bandit (MAB) algorithms identify the best arm among multiple arms via exploration-exploitation trade-off without prior knowledge of arm statistics. Their usefulness in wireless radio, Internet of Things (IoT), and robotics demand deployment on edge devices, and hence, a mapping on system-on-chip (SoC) is desired. Theoretically, the Bayesian-approach-based Thompson sampling (TS) algorithm offers better performance than the frequentist-approach-based upper confidence bound (UCB) algorithm. However, TS is not synthesizable due to Beta function. We address this problem by approximating it via a pseudorandom number generator (PRNG)-based architecture and efficiently realize the TS algorithm on Zynq SoC. In practice, the type of arms distribution (e.g., Bernoulli, Gaussian) is unknown, and hence, a single algorithm may not be optimal. We propose a reconfigurable and intelligent MAB (RI-MAB) framework. Here, intelligence enables the identification of appropriate MAB algorithms in an unknown environment, and reconfigurability allows on-the-fly switching between algorithms on the SoC. This eliminates the need for parallel implementation of algorithms resulting in huge savings in resources and power consumption. We analyze the functional correctness, area, power, and execution time of the proposed and existing architectures for various arm distributions, word length, and hardware-software codesign approaches. We demonstrate the superiority of the RI-MAB algorithm and its architecture over the TS and UCB algorithms.

PMID:35853057 | DOI:10.1109/TNNLS.2022.3190509

PLoS One. 2022 Jul 19;17(7):e0271232. doi: 10.1371/journal.pone.0271232. eCollection 2022.

ABSTRACT

BACKGROUND: Cysticercosis and Neurocysticercosis (NCC) can be studied using several animal species in experimental models which contributes to the understanding of the human form of the disease. Experimental infections of Taenia spp. are vital in explaining the modes of transmission of the parasite and helps the understanding of transmission of the parasite in humans and thus may be useful in designing therapeutic and immune-prophylactic studies to combat the disease. Thus, this systematic review aims to explore the existing experimental animal models to the understanding of cysticercosis in both humans and animals and elucidate the risk factors of cysticercosis and identify the Taenia spp. used in these models.

METHODOLOGY: We systematically identified all publications from the Web of Science, Google Scholar, and Pubmed regarding experimental animal models using Taenia spp. that cause cysticercosis in both humans and animals. 58 studies were identified for eligibility. Of these, only 48 studies met the inclusion criteria from which data extraction was done and presented descriptively.

RESULTS: Pigs, cattle, gerbils, mice, rats, voles, monkeys, cats, dogs, and goats were used in which T. solium, T. saginata, T. saginata asiatica, T. crassiceps and T. asiatica were studied. The routes used to induce disease were; oral, intravenous, subcutaneous, intramuscular, intraperitoneal, intraarterial, intracranial, intraduodenal, and surgical routes using eggs, oncospheres, and proglottids. Besides, the establishment of infection using eggs and oncospheres was affected by the route used to induce infection in the experimental animals. The cysticerci recovery rate in all the experimental studies was low and the number of animals used in these experiments varied from 1 to 84. Although not analysed statistically, sex, age, and breed of animals influenced the cysticerci recovery rate. Additionally, the cysticerci recovery rate and antibody-antigen levels were shown to increase with an increase in the dose of oncospheres and eggs inoculated in the animals. Contrasting results were reported in which the cysticerci recovery rate decreased with an increase in the dose of eggs inoculated.

CONCLUSION: This review describes the various animal experiments using Taenia species that cause cysticercosis highlighting the animals used, age and their breed, the routes of infection used to induce disease and the sample size used, and the cysticerci recovery rate in these animal models.

PMID:35853079 | DOI:10.1371/journal.pone.0271232

PLoS One. 2022 Jul 19;17(7):e0269930. doi: 10.1371/journal.pone.0269930. eCollection 2022.

ABSTRACT

New Zealand’s Prime Minister, Jacinda Ardern, adopted a “go hard, go early” approach to eliminate COVID-19. Although Ardern and her Labour party are considered left-leaning, the policies implemented during the pandemic (e.g., police roadblocks) have the hallmarks of Right-Wing Authoritarianism (RWA). RWA is characterized by three attitudinal clusters (authoritarian aggression, submission, and conventionalism). The uniqueness of the clusters, and whether they react to environmental change, has been debated. Here, in the context of the pandemic, we investigate the relationship between political orientation and RWA. Specifically, we measured political orientation, support for New Zealand’s major political parties, and RWA among 1,430 adult community members. A multivariate Bayesian model demonstrated that, in the middle of a pandemic, both left-leaning and right-leaning individuals endorsed items tapping authoritarian submission. In contrast to authoritarian submission, and demonstrating the multidimensional nature of RWA, we observed the typical relationships between political orientation and authoritarian aggression and conventionalism was observed.

PMID:35853036 | DOI:10.1371/journal.pone.0269930

PLoS One. 2022 Jul 19;17(7):e0271319. doi: 10.1371/journal.pone.0271319. eCollection 2022.

ABSTRACT

Socio-economic and geographical inequalities in breast cancer mortality have been widely described in European countries and the United States. To investigate the combined effects of geographic access and socio-economic characteristics on breast cancer outcomes, a systematic review was conducted exploring the relationships between: (i) geographic access to healthcare facilities (oncology services, mammography screening), defined as travel time and/or travel distance; (ii) breast cancer-related outcomes (mammography screening, stage of cancer at diagnosis, type of treatment and rate of mortality); (iii) socioeconomic status (SES) at individuals and residential context levels. In total, n = 25 studies (29 relationships tested) were included in our systematic review. The four main results are: The statistical significance of the relationship between geographic access and breast cancer-related outcomes is heterogeneous: 15 were identified as significant and 14 as non-significant. Women with better geographic access to healthcare facilities had a statistically significant fewer mastectomy (n = 4/6) than women with poorer geographic access. The relationship with the stage of the cancer is more balanced (n = 8/17) and the relationship with cancer screening rate is not observed (n = 1/4). The type of measures of geographic access (distance, time or geographical capacity) does not seem to have any influence on the results. For example, studies which compared two different measures (travel distance and travel time) of geographic access obtained similar results. The relationship between SES characteristics and breast cancer-related outcomes is significant for several variables: at individual level, age and health insurance status; at contextual level, poverty rate and deprivation index. Of the 25 papers included in the review, the large majority (n = 24) tested the independent effect of geographic access. Only one study explored the combined effect of geographic access to breast cancer facilities and SES characteristics by developing stratified models.

PMID:35853035 | DOI:10.1371/journal.pone.0271319

PLoS One. 2022 Jul 19;17(7):e0269950. doi: 10.1371/journal.pone.0269950. eCollection 2022.

ABSTRACT

PURPOSE: Breast cancer is one of the most common tumours in women, nevertheless, it is also one of the cancers that is most usually treated. As a result, early detection is critical, which can be accomplished by routine mammograms. This paper aims to describe, analyze, compare and evaluate three image descriptors involved in classifying breast cancer images from four databases.

APPROACH: Multi-Objective Evolutionary Algorithms (MOEAs) prove themselves as being efficient methods for selection and classification problems. This paper aims to study combinations of well-known classification objectives in order to compare the results of their application in solving very specific learning problems. The experimental results undergo empirical analysis which is supported by a statistical approach. The results are illustrated on a collection of medical image databases, but with a focus on the MOEAs’ performance in terms of several well-known measures. The databases were chosen specifically to feature reliable human annotations, so as to measure the correlation between the gold standard classifications and the various MOEA classifications.

RESULTS: We have seen how different statistical tests rank one algorithm over the others in our set as being better. These findings are unsurprising, revealing that there is no single gold standard for comparing diverse techniques or evolutionary algorithms. Furthermore, building meta-classifiers and evaluating them using a single, favorable metric is both extremely unwise and unsatisfactory, as the impact is to skew the results.

CONCLUSIONS: The best method to address these flaws is to select the right set of objectives and criteria. Using accuracy-related objectives, for example, is directly linked to maximizing the number of true positives. If, on the other hand, accuracy is chosen as the generic metric, the primary classification goal is shifted to increasing the positively categorized data points.

PMID:35853014 | DOI:10.1371/journal.pone.0269950

PLoS One. 2022 Jul 19;17(7):e0271491. doi: 10.1371/journal.pone.0271491. eCollection 2022.

ABSTRACT

BACKGROUND: There is little research on how financial incentives and penalties impact national cesarean section rates. In January 2018, Georgia introduced a national cesarean section reduction policy, which imposes a financial penalty on hospitals that do not meet their reduction targets. The aim of this study was to assess the impact of this policy on cesarean section rates, subgroups of women, and selected perinatal outcomes.

METHODS: We included women who gave birth from 2017 to 2019 registered in the Georgian Birth Registry (n = 150 534, nearly 100% of all births in the country during this time). We then divided the time period into pre-policy (January 1, 2017, to December 31, 2017) and post-policy (January 1, 2018, to December 31, 2019). An interrupted time series analysis was used to compare the cesarean section rates (both overall and stratified by parity), neonatal intensive care unit transfer rates, and perinatal mortality rates in the two time periods. Descriptive statistics were used to assess differences in maternal socio-demographic characteristics.

RESULTS: The mean cesarean section rate in Georgia decreased from 44.7% in the pre-policy period to 40.8% in the post-policy period, mainly among primiparous women. The largest decrease in cesarean section births was found among women <25 years of age and those with higher education. There were no significant differences in the neonatal intensive care unit transfer rate or the perinatal mortality rate between vaginal and cesarean section births in the post-policy period.

CONCLUSION: The cesarean section rate in Georgia decreased during the 2-year post-policy period. The reduction mainly took place among primiparous women. The policy had no impact on the neonatal intensive care unit transfer rate or the perinatal mortality rate. The impact of the national cesarean section reduction policy on other outcomes is not known.

PMID:35853028 | DOI:10.1371/journal.pone.0271491

PLoS One. 2022 Jul 19;17(7):e0271480. doi: 10.1371/journal.pone.0271480. eCollection 2022.

ABSTRACT

INTRODUCTION: Parkinson’s disease is a motor disease, the second most common neurodegenerative disorder with cardinal symptoms including bradykinesia, rigidity, and rest tremor accompanied by cognitive difficulties. The caregivers play a crucial role for individuals with Parkinson’s disease; however, many of them may suffer from high caregiver burden and mental health deterioration. This protocol of a systematic review presents a methodology of the review about the impact of cognitive impairment of individuals with Parkinson’s disease on their caregivers’ mental health.

MATERIAL AND METHODS: Research will be identified by combining electronic databases searching and hand searching. The following databases will be included: Medline, PsycInfo, Web of Sciences, Cochrane, CINAHL, Embase and Scopus. The inclusion and exclusion criteria followed to PECOS model. The population of informal caregivers is defined as family members providing care on a patient with Parkinson’s disease. Exposure is linked with the evaluation of a cognitive functioning and outcome is defined as mental health among caregivers of individuals with Parkinson’s disease. We will include two types of studies: observational and intervention. Both, screening and eligibility will be done by two independent reviewers. Study quality will be assessed by two authors independently. Data will be extracted by two reviewers independently and will follow a pre-pilot extraction form. Any discrepancies will be resolved by discussion or/and consultation with another reviewer. The synthesis without meta-analysis (SWiM) guidelines will be used to report on included studies data. The metanalysis with usage the statistical software R version 4.1.2 (2021-11-01) “Bird Hippie” and R metaphor package 3.0-2 of will be conducted if possible.

DISCUSSION: The goal of this systematic review is to present the association between caregivers’ mental health problems and their proteges’ cognitive impairment. It will enable to identify the gaps in literature and its methodology giving the suggestions for further research.

PROTOCOL REGISTRATION: Protocol registration number in PROSPERO: CRD42022296670.

PMID:35853013 | DOI:10.1371/journal.pone.0271480