Tag: statistics

Med Phys. 2021 Jul 27. doi: 10.1002/mp.15133. Online ahead of print.

ABSTRACT

PURPOSE: The global noise (GN) algorithm has been previously introduced as a method for automatic noise measurement in clinical CT images. Accuracy of the GN algorithm has been assessed in abdomen CT exams, but not in any other body part until now. This work assesses the GN algorithm accuracy in automatic noise measurement in head CT exams.

METHODS: A publicly available image dataset of 99 head CT exams was used to evaluate the accuracy of the GN algorithm in comparison to reference noise values. Reference noise values were acquired using a manual noise measurement procedure. The procedure used a consistent instruction protocol and multiple observers to miti-gate the influence of intra- and inter-observer variation, resulting in precise reference values. Optimal GN algorithm parameter values were determined. The GN algorithm accuracy and the corresponding statistical confidence interval were determined. The GN measurements were compared across the 6 different scan protocols used in this dataset. The correlation of GN to patient head size was also assessed using a linear regression model, and the CT scanner’s x-ray beam quality was inferred from the model fit parameters.

RESULTS: Across all head CT exams in the dataset, the range of reference noise was 2.9 – 10.2 HU. A precision of ±0:33 HU was achieved in the reference noise measurements. After optimization, then GN algorithm had a RMS error 0.34 HU corresponding to a percent RMS error of 6.6%. The GN algorithm had a bias of +3.9%. Statistically significant differences in GN were detected in 11 out of the 15 different pairs of scan protocols. The GN measurements were correlated with head size with a statistically significant regression slope parameter (p < 10^-7 ). The CT scanner x-ray beam quality estimated from the slope parameter was 3.5 cm water HVL (2.8{4.8 cm 95% C.I.).

CONCLUSION: The GN algorithm was validated for application in head CT exams. The GN algorithm was accurate in comparison to reference manual measurement, with errors comparable to inter-observer variation in manual measurement. The GN algorithm can detect noise differences in exams performed on different scanner models or using different scan protocols. The trend of GN across patients of different head sizes closely follows that predicted by a physical model of x-ray attenuation.

PMID:34314528 | DOI:10.1002/mp.15133

Acta Paediatr. 2021 Jul 27. doi: 10.1111/apa.16045. Online ahead of print.

ABSTRACT

AIM: To compare risk-algorithms (HCMRisk-Kids, ECG Risk-score) in hypertrophic cardiomyopathy (HCM) without syndrome association (ns-HCM), and with Noonan-like syndromes (RAS-HCM).

METHODS: A national paediatric HCM-cohort (n=151), presenting <19y of age, mean follow-up 13.3y, from all Swedish centres of Paediatric Cardiology (presenting 1972-2015), with 41 RAS-HCM-patients (61% males), and 110 ns-HCM-patients (68% familial; 65% males). The end-point was a composite of sudden cardiac death and re-suscitated cardiac arrest (SCD/CA). Risk-factors were studied with Cox-hazard regression, and ROC-curve analysis (C-statistic).

RESULTS: There were 33 SCD/CA, 27/110 in ns-HCM and 6/41 in RAS-HCM (p=0.27). In ns-HCM HCMRisk-Kids ≥6% at diagnosis had C-statistic of 0.69 for predicting SCD/CA during first 5y of follow-up, and positive predictive value (PPV) of 22%. After 7y of age (HCMRisk-Kids7plus) C-statistic was 0.76. ECG Risk-score ≥6 at diagnosis had C-statistic 0.87 and PPV of 31%. Independent risk factors for SCD/CA were HCMRisk-Kids7plus score (p=0.005) and ECG risk-score (p<0.001), whereas early beta-blocker dose (p=0.001) and myectomy (p=0.004) reduced risk. The sum of HCMRisk-Kids7yplus and ECG Risk-score7yplus ≥14 best predicted SCD/CA within 5y in ns-HCM with C-statistic of 0.90 [0.83-0.96], sensitivity 100%, and PPV 38%.

CONCLUSIONS: Combining the ECG Risk-score with HCMRisk-Kids improves risk-stratification in ns-HCM, and shows promise in RAS-HCM.

PMID:34314540 | DOI:10.1111/apa.16045

PLoS One. 2021 Jul 27;16(7):e0255235. doi: 10.1371/journal.pone.0255235. eCollection 2021.

ABSTRACT

BACKGROUND: Emerging data suggest a negative role of cyclooxygenase-2 (COX-2) in colorectal carcinomas (CRC). Investigating this in developing communities such as ours helps to contribute to existing understanding of these lesions.

METHODS AND FINDINGS: Formalin-fixed paraffin-embedded CRC colectomy tissues and their corresponding non-tumour margins of resected tissues were sectioned and stained with COX-2 antibody. Adenomatous polyp tissues from non-cancer bearing individuals were similarly processed for comparison. COX-2 expression was scored for percentage (< 5% = 0; 6%-25% = 1; 26%-50% = 2; 51%-75% = 3; 76%-100% = 4) and intensity (no staining = 0; yellow = 2; yellowish-brown = 3, brown = 4). Total immunoscore (percentage + intensity score) ≥ 2 was regarded as positive COX-2 expression. Outcome was statistically evaluated with clinicopathological data to determine COX-2 expression-associated and predictor variables. Ninety-five CRC cases and 27 matched non-tumour tissues as well as 31 adenomatous polyps met the inclusion criteria. Individuals with CRC had a mean age of 56.1 ± 12.6 years while those with adenomatous polyps had a median age of 65 years (range 43-88). COX-2 was differentially overexpressed in CRCs (69/95; 72.6%) and in adenomatous polyps (17/31; 54.8%) than in non-tumour tissues 5/27 (18.5%); p < 0.001). The difference in COX-2 expression between CRC and polyps was non-significant (p > 0.065). Tumour grade, advanced pT-stage, tumour-infiltrating lymphocytes, and dirty necrosis were also significantly associated with COX-2 expression (p < 0.035; 0.043, 0.035 and 0.004, respectively). Only dirty necrosis and Crohns-like lymphocytic aggregates predicted COX-2 expression (p < 0.05).

CONCLUSION: This study showed a progressive increase in COX-2 expression from normal to adenomatous polyp and CRC tissues, this being associated with poorer prognostic indicators. Although COX-2 appears early in CRC, it may play a secondary role in promoting tumour growth and invasiveness.

PMID:34314467 | DOI:10.1371/journal.pone.0255235

Int J Gynaecol Obstet. 2021 Jul 27. doi: 10.1002/ijgo.13838. Online ahead of print.

ABSTRACT

OBJECTIVE: To assess the differences in Doppler parameters of endometrial receptivity in unexplained recurrent biochemical pregnancy loss (URBPL) and the therapeutic effect of low-dose aspirin (LDA).

METHODS: A retrospective study was conducted at Ren Ji Hospital, Shanghai, PR China, from January 2017 to January 2019. Doppler parameters of endometrium and uterus were recorded as the evaluation of the endometrial receptivity. Receiver operating characteristic (ROC) curve was managed to predict the risk of URBPL. Ultrasonography tests were repeated after 2 months of treatment with LDA.

RESULTS: Biochemical pregnancies did not correlate with maternal age. The resistance of endometrial perfusion (pulsatility index, resistive index, and systolic-to-diastolic ratio) was significantly higher in URBPLs (P<0.001) and had predictive values (0.739, 0.779, and 0.760, respectively). Endometrial thickness and impedance to uterine blood flow showed no statistically significant difference (P>0.05). After treatment with LDA, patients with URBPL improved the blood perfusion of endometrium significantly (P<0.01).

CONCLUSION: There was no relation between BPL and maternal age. Patients with URBPL had inappropriate endometrial blood velocity. Doppler indices are capable of predicting the risk of URBPL. LDA exerts the therapeutic effect on improving blood perfusion of endometrium in URBPL.

PMID:34314517 | DOI:10.1002/ijgo.13838

PLoS One. 2021 Jul 27;16(7):e0255290. doi: 10.1371/journal.pone.0255290. eCollection 2021.

ABSTRACT

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower’s genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

PMID:34314448 | DOI:10.1371/journal.pone.0255290

PLoS One. 2021 Jul 27;16(7):e0255203. doi: 10.1371/journal.pone.0255203. eCollection 2021.

ABSTRACT

BACKGROUND: Behavioural patterns are typically derived using unsupervised multivariate methods such as principal component analysis (PCA), latent profile analysis (LPA) and cluster analysis (CA). Comparability and congruence between the patterns derived from these methods has not been previously investigated, thus it’s unclear whether patterns from studies using different methods are directly comparable. This study aimed to compare behavioural patterns derived across diet, physical activity, sedentary behaviour and sleep domains, using PCA, LPA and CA in a single dataset.

METHODS: Parent-report and accelerometry data from the second wave (2011/12; child age 6-8y, n = 432) of the HAPPY cohort study (Melbourne, Australia) were used to derive behavioural patterns using PCA, LPA and CA. Standardized variables assessing diet (intake of fruit, vegetable, sweet, and savoury discretionary items), physical activity (moderate- to vigorous-intensity physical activity [MVPA] from accelerometry, organised sport duration and outdoor playtime from parent report), sedentary behaviour (sedentary time from accelerometry, screen time, videogames and quiet playtime from parent report) and sleep (daily sleep duration) were included in the analyses. For each method, commonly used criteria for pattern retention were applied.

RESULTS: PCA produced four patterns whereas LPA and CA each generated three patterns. Despite the number and characterisation of the behavioural patterns derived being non-identical, each method identified a healthy, unhealthy and a mixed pattern. Three common underlying themes emerged across the methods for each type of pattern: (i) High fruit and vegetable intake and high outdoor play (“healthy”); (ii) poor diet (either low fruit and vegetable intake or high discretionary food intake) and high sedentary behaviour (“unhealthy”); and (iii) high MVPA, poor diet (as defined above) and low sedentary time (“mixed”).

CONCLUSION: Within this sample, despite differences in the number of patterns derived by each method, a good degree of concordance across pattern characteristics was seen between the methods. Differences between patterns could be attributable to the underpinning statistical technique of each method. Therefore, acknowledging the differences between the methods and ensuring thorough documentation of the pattern derivation analyses is essential to inform comparison of patterns derived through a range of approaches across studies.

PMID:34314443 | DOI:10.1371/journal.pone.0255203

PLoS One. 2021 Jul 27;16(7):e0255026. doi: 10.1371/journal.pone.0255026. eCollection 2021.

ABSTRACT

Building capacity for developing skills as leadership, teamwork, and continuous academic support has become essential for fulfilling a successful pharmacy career. This study aims to assess Jordanian pharmacists’ views on professional development, namely: the continuous education infrastructure, strategies and programs for personal development, leadership skills, incentive schemes, drug information resources and digital services. As well as exploring options for better academic support delivered to pharmacists. To capture participant’s views, an online validated and reliable survey was developed. Non-probability sampling design was used. Participants were qualified pharmacists working at Royal Medical Services (RMS) and Community Pharmacists (CP). Comparison and descriptive statistics were used to report the results. A total of 271 pharmacists participated, 144 from RMS (8% more than the needed sample) and 127 CP (7% more than the needed sample). There was a strong desire amongst both RMS and PC groups for continuous educational training particularly in the following areas, first: Advanced counselling and communication skills (means = 8.99±0.145, CI 95% = 3.70-4.28 and 9.37±0.096, CI 95% = 4.18-4.56). Second: Personal development skills (mean = 8.92±0.142, CI 95% = 3.64-4.20 and 9.02±0.145, CI 95% = 3.73-4.30). Third, Pharmaceutical health promotion (mean = 8.05±0.180, CI 95% = 2.70-3.41 and 8.57±0.159, CI 95% = 3.26-3.89). Only 19.4% and 18.1% of the RMS and CPs respectively reported the presence of a written policy for personal development and leadership in their workplace. There were few incentives for pharmacists to participate in research. Few pharmacists used the available drug information and toxicology centers. The professional and continuous personal development of pharmacists support an evolving healthcare system. This study emphasizes the need for a tailored and documented postgraduate educational strategy, personal development, and leadership skills training in Jordan. Implementing a well-defined scheme of incentives should be encouraged to engage pharmacists in continuous professional development programs and pharmaceutical research. Such strategy and training should enhance both professional and personal performance.

PMID:34314444 | DOI:10.1371/journal.pone.0255026

PLoS One. 2021 Jul 27;16(7):e0255379. doi: 10.1371/journal.pone.0255379. eCollection 2021.

ABSTRACT

BACKGROUND: The hematological abnormalities are assumed to be involved in the disease progression of COVID-19. However, the actual associations between specific blood parameters and COVID-19 are not well understood. Here we aimed to assess the correlations between hematological parameters and the severity of COVID-19.

METHODS: We included COVID-19 patients who were admitted to Evercare Hospital Ltd, Dhaka, Bangladesh, between November 10, 2020, to April 12, 2021, with a confirmed case of RT-PCR test. We recorded demographic information, clinical data, and routine hematological examination results of all COVID-19 patients. We performed statistical analyses and interpretation of data to compare severe COVID-19 patients (SCP) and non-severe COVID-19 patients (NSCP).

RESULTS: The age and BMI of the admitted COVID-19 patients were 48.79±8.53 years and 25.82±3.75 kg/m2. This study included a total of 306 hospitalized COVID-19 patients. Among them, NSCP and SCP were 198 and 108, respectively. And we recorded 12 deaths from SCP. We observed the alterations of several hematological parameters between SCP and NSCP. Among them, we noticed the increased levels of C-reactive protein (CRP), d-dimer, and ferritin showed good indicative value to evaluate the severity of COVID-19. Also, there were positive correlations among these parameters. Moreover, we found correlations between the outcomes of COVID-19 patients with patient’s demographics and comorbid diseases.

CONCLUSION: Based on our results, CRP, d-dimer, and ferritin levels at admission to hospitals represent simple assessment factors for COVID-19 severity and the treatment decisions at the hospital setup. These blood parameters could serve as indicators for the prognosis and severity of COVID-19. Therefore, our study findings might help to develop a treatment protocol for COVID-19 patients at the hospital setup.

PMID:34314447 | DOI:10.1371/journal.pone.0255379

PLoS Genet. 2021 Jul 27;17(7):e1009684. doi: 10.1371/journal.pgen.1009684. Online ahead of print.

ABSTRACT

Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans-eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk variant for autoimmune disease, rs17622517 in an intron of C5ORF56, affects the expression of the transcription factor IRF1 20 kb away. The cis-regulatory effect specific to IRF1 is active under early immune stimulus, with a large number of trans-eQTL effects across the genome under late LPS response. Using CRISPRi silencing, we showed that perturbation of the SNP locus downregulates IRF1 and causes widespread transcriptional effects. Genome editing by CRISPR had suggestive recapitulation of the LPS-specific trans-eQTL signal and lent support for the rs17622517 site being functional. Our results suggest that this common genetic variant affects inter-individual response to immune stimuli via regulation of IRF1. For this autoimmune GWAS locus, our work provides evidence of the functional variant, demonstrates a condition-specific enhancer effect, identifies IRF1 as the likely causal gene in cis, and indicates that overactivation of the downstream immune-related pathway may be the cellular mechanism increasing disease risk. This work not only provides rare experimental validation of a master-regulatory trans-eQTL, but also demonstrates the power of eQTL mapping to build mechanistic hypotheses amenable for experimental follow-up using the CRISPR toolkit.

PMID:34314424 | DOI:10.1371/journal.pgen.1009684

PLoS Negl Trop Dis. 2021 Jul 27;15(7):e0009647. doi: 10.1371/journal.pntd.0009647. Online ahead of print.

ABSTRACT

BACKGROUND: The sand fly Phlebotomus perniciosus is the main vector of Leishmania infantum, etiological agent of zoonotic visceral leishmaniasis in the Western Mediterranean basin. Dogs are the main reservoir host of this disease. The main objective of this study was to determine, under both laboratory and field conditions, if dogs infected with L. infantum, were more attractive to female P. perniciosus than uninfected dogs.

METHODOLOGY/PRINCIPAL FINDINGS: We carried out a series of host choice experiments and found that infected dogs were significantly more attractive to P. perniciosus than uninfected dogs in the laboratory as well as in the field. Significantly more P. perniciosus fed on infected dogs than on uninfected dogs. However, the fecundity of P. perniciosus fed on infected dogs was adversely impacted compared to uninfected dogs by lowering the number of laid eggs. Phlebotomus perfiliewi, the second most abundant sand fly species in the field site and a competent vector of L. infantum had similar trends of attractivity as P. perniciosus toward infected dogs under field conditions.

CONCLUSIONS: The results strongly suggest that L. infantum causes physiological changes in the reservoir host which lead to the host becoming more attractive to both male and female P. perniciosus. These changes are likely to improve the chance of successful transmission because of increased contact with infected hosts and therefore, infected dogs should be particularly targeted in the control of zoonotic visceral leishmaniasis in North Africa.

PMID:34314425 | DOI:10.1371/journal.pntd.0009647