Tag: pubmed

Med Image Anal. 2021 Jul 18;73:102164. doi: 10.1016/j.media.2021.102164. Online ahead of print.

ABSTRACT

[Background] Electromagnetically Navigated Bronchoscopy (ENB) is currently the state-of-the art diagnostic and interventional bronchoscopy. CT-to-body divergence is a critical hurdle in ENB, causing navigation error and ultimately limiting the clinical efficacy of diagnosis and treatment. In this study, Visually Navigated Bronchoscopy (VNB) is proposed to address the aforementioned issue of CT-to-body divergence. [Materials and Methods] We extended and validated an unsupervised learning method to generate a depth map directly from bronchoscopic images using a Three Cycle-Consistent Generative Adversarial Network (3cGAN) and registering the depth map to preprocedural CTs. We tested the working hypothesis that the proposed VNB can be integrated to the navigated bronchoscopic system based on 3D Slicer, and accurately register bronchoscopic images to pre-procedural CTs to navigate transbronchial biopsies. The quantitative metrics to asses the hypothesis we set was Absolute Tracking Error (ATE) of the tracking and the Target Registration Error (TRE) of the total navigation system. We validated our method on phantoms produced from the pre-procedural CTs of five patients who underwent ENB and on two ex-vivo pig lung specimens. [Results] The ATE using 3cGAN was 6.2 +/- 2.9 [mm]. The ATE of 3cGAN was statistically significantly lower than that of cGAN, particularly in the trachea and lobar bronchus (p < 0.001). The TRE of the proposed method had a range of 11.7 to 40.5 [mm]. The TRE computed by 3cGAN was statistically significantly smaller than those computed by cGAN in two of the five cases enrolled (p < 0.05). [Conclusion] VNB, using 3cGAN to generate the depth maps was technically and clinically feasible. While the accuracy of tracking by cGAN was acceptable, the TRE warrants further investigation and improvement.

PMID:34314953 | DOI:10.1016/j.media.2021.102164

J Environ Manage. 2021 Jul 24;297:113344. doi: 10.1016/j.jenvman.2021.113344. Online ahead of print.

ABSTRACT

Although the effect of digital elevation model (DEM) and its spatial resolution on flood simulation modeling has been well studied, the effect of coarse and finer resolution image and DEM data on machine learning ensemble flood susceptibility prediction has not been investigated, particularly in data sparse conditions. The present work was, therefore, to investigate the performance of the resolution effects, such as coarse (Landsat and SRTM) and high (Sentinel-2 and ALOS PALSAR) resolution data on the flood susceptible models. Another motive of this study was to construct very high precision and robust flood susceptible models using standalone and ensemble machine learning algorithms. In the present study, fifteen flood conditioning parameters were generated from both coarse and high resolution datasets. Then, the ANN-multilayer perceptron (MLP), random forest (RF), bagging (B)-MLP, B-gaussian processes (B-GP) and B-SMOreg algorithms were used to integrate the flood conditioning parameters for generating the flood susceptible models. Furthermore, the influence of flood conditioning parameters on the modelling of flood susceptibility was investigated by proposing an ROC based sensitivity analysis. The validation of flood susceptibility models is also another challenge. In the present study, we proposed an index of flood vulnerability model to validate flood susceptibility models along with conventional statistical techniques, such as the ROC curve. Results showed that the coarse resolution based flood susceptibility MLP model has appeared as the best model (area under curve: 0.94) and it has predicted 11.65 % of the area as very high flood susceptible zones (FSz), followed by RF, B-MLP, B-GP, and B-SMOreg. Similarly, the high resolution based flood susceptibility model using MLP has predicted 19.34 % of areas as very high flood susceptible zones, followed by RF (14.32 %),B-MLP (14.88 %), B-GP, and B-SMOreg. On the other hand, ROC based sensitivity analysis showed that elevation influences flood susceptibility largely for coarse and high resolution based models, followed by drainage densityand flow accumulation. In addition, the accuracy assessment using the IFV model revealed that the MLP model outperformed all other models in the case of a high resolution imageThe coarser resolution image’s performance level is acceptable but quite low. So, the study recommended the use of high resolution images for developing a machine learning algorithm based flood susceptibility model. As the study has clearly identified the areas of higher flood susceptibility and the dominant influencing factors for flooding, this could be used as a good database for flood management.

PMID:34314957 | DOI:10.1016/j.jenvman.2021.113344

Nutrition. 2021 Jun 24;91-92:111391. doi: 10.1016/j.nut.2021.111391. Online ahead of print.

ABSTRACT

OBJECTIVE: Observational epidemiologic studies have reported a relationship between selenium status and risk for autoimmune diseases. However, the associations are susceptible to confounding or reverse causality. Thus, the aim of this study was to investigate the potential causal associations of selenium concentrations with the risk for common autoimmune diseases using a two-sample Mendelian randomization (MR) design.

METHODS: A meta-analysis of genome-wide association studies (GWASs) of selenium among 9639 individuals of European ancestry was used to identify genetic instruments. Summary statistics of systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease were obtained from publicly available GWASs, respectively. We conducted MR study using the inverse-variance weighted method, supplemented with weighted median and likelihood-based methods as sensitivity analysis. Cochran Q test and MR-Egger regression were used to detect heterogeneity and potential directional pleiotropy. MR-Pleiotropy RESidual Sum and Outlier test was used to identify outlier single-nucleotide polymorphisms.

RESULTS: Genetically predicted high selenium level was associated with a decreased risk for SLE (odds ratio, 0.85; 95% confidence interval, 0.77-0.93; P = 0.001) per natural log-transformed selenium concentrations, with similar results in sensitivity analyses. No evidence of heterogeneity, pleiotropy, or outlier single-nucleotide polymorphisms were detected (all P > 0.05). However, genetically determined selenium concentrations may be not associated with risk for rheumatoid arthritis or inflammatory bowel disease in the primary analysis and subsequent sensitivity analyses.

CONCLUSIONS: The present study suggested a protective role of selenium on the risk for systemic lupus erythematosus. Further studies are warranted to elucidate the underlying mechanisms.

PMID:34314985 | DOI:10.1016/j.nut.2021.111391

J Evol Biol. 2021 Jul 27. doi: 10.1111/jeb.13906. Online ahead of print.

ABSTRACT

Although consistent between-individual differences in behaviour (i.e. animal personality) are ubiquitous in natural populations, relatively few studies have examined how personalities influence the formation of social relationships. Yet, behavioural characteristics of both sexes might be key when it comes to pair-bond formation, and the cooperation with partners to successfully rear offspring. We here use a wild population of dunnocks (Prunella modularis) to first investigate whether individuals mate non-randomly (i.e. assortative mating) with regard to four behavioural traits – flight-initiation distance (FID), provisioning, activity, and vigilance – that differ in repeatability and have previously been associated with mating patterns and fitness in other species. Second, we test whether an individual’s FID is associated with variability in the dunnocks’ mating system (i.e. monogamous pairs vs. polygamous groups). Finally, we determine whether FID and provisioning of males and females associate with their reproductive success. We found no statistical support for assortative mating in FID between males and females. Interestingly, in polygamous groups, co-breeding males differed in their FIDs with dominant alpha-males having significantly shorter FIDs compared to subordinate beta-males. Moreover, there was evidence for assortative mating in provisioning for alpha-males and females in polygamous groups. We also found that male provisioning influenced reproductive success of both sexes, while female provisioning rates only positively correlated with her own but not their partner(s) reproductive output. Our results suggest that personality differences may have important implications for social relationships, the emergence of different mating patterns and ultimately reproductive success within populations.

PMID:34314544 | DOI:10.1111/jeb.13906

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