Consistency Of Different Methods Research Articles

The repeatability and consistency of different methods for measuring the volume parameters of the primary rectal cancer on diffusion weighted images.

To determine the reproducibility of measuring the gross total volume (GTV) of primary rectal tumor with manual and semi-automatic delineation on the diffusion-weighted image (DWI), examine the consistency of using the same delineation method on DWI images with different high b-values, and find the optimal delineation method to measure the GTV of rectal cancer. 41 patients who completed rectal MR examinations in our hospital from January 2020 to June 2020 were prospectively enrolled in this study. The post-operative pathology confirmed the lesions were rectal adenocarcinoma. The patients included 28 males and 13 females, with an average age of (63.3 ± 10.6) years old. Two radiologists used LIFEx software to manually delineate the lesion layer by layer on the DWI images (b=1000 s/mm2 and 1500 s/mm2) and used 10% to 90% of the highest signal intensity as thresholds to semi-automatically delineate the lesion and measure the GTV. After one month, Radiologist 1 performed the same delineation work again to obtain the corresponding GTV. The inter- and intra-observer interclass correlation coefficients (ICC) of measuring GTV using semi-automatic delineation with 30% to 90% as thresholds were all >0.900. There was a positive correlation between manual delineation and semi-automatic delineation with 10% to 50% thresholds (P < 0.05). However, the manual delineation was not correlated with the semi-automatic delineation with 60%, 70%, 80%, and 90% thresholds. On the DWI images with b=1000 s/mm2 and 1500 s/mm2, the 95% limit of agreement (LOA%) of measuring GTV using semi-automatic delineation with 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, and 90% thresholds were -41.2~67.4, -17.8~51.5, -16.1~49.3, -26.2~50.1, -42.3~57.6, -57.1~65.4, -67.3~66.5, -101.6~91.1, -129.4~136.0, and -15.3~33.0, respectively. The time required for GTV measurement by semi-automatic delineation was significantly shorter than that of manual delineation (12.9 ± 3.6s vs 40.2 ± 13.1s). The semi-automatic delineation of rectal cancer GTV with 30% threshold had high repeatability and consistency, and it was positively correlated with the GTV measured by manual delineation. Therefore, the semi-automatic delineation with 30% threshold could be a simple and feasible method for measuring rectal cancer GTV.

Neural network interpretation techniques for analysis of histological images of breast abnormalities

Background. Neural networks are actively used in digital pathology to analyze histological images and support medical decision-making. A common approach is to solve the classification problem, where only class labels are the only model responses. However, one should understand which areas of the image have the most significant impact on the model's response. Machine learning interpretation techniques help solve this problem.&#x0D; Aim. To study the consistency of different methods of neural network interpretation when classifying histological images of the breast and to obtain an expert assessment of the results of the evaluated methods.&#x0D; Materials and methods. We performed a preliminary analysis and pre-processing of the existing data set used to train pre-selected neural network models. The existing methods of visualizing the areas of attention of trained models on easy-to-understand data were applied, followed by verification of their correct use. The same neural network models were trained on histological data, and the selected interpretation methods were used to systematize histological images, followed by the evaluation of the results consistency and an expert assessment of the results.&#x0D; Results. In this paper, several methods of interpreting machine learning are studied using two different neural network architectures and a set of histological images of breast abnormalities. Results of ResNet18 and ViT-B-16 models training on a set of histological images on the test sample: accuracy metric 0.89 and 0.89, ROC_AUC metric 0.99 and 0.96, respectively. The results were also evaluated by an expert using the Label Studio tool. For each pair of images, the expert was asked to select the most appropriate answer ("Yes" or "No") to the question: "The highlighted areas generally correspond to the Malignant class." The "Yes" response rate for the ResNet_Malignant category was 0.56; for ViT_Malignant, it was 1.0.&#x0D; Conclusion. Interpretability experiments were conducted with two different architectures: the ResNet18 convolutional network and the ViT-B-16 attention-enhanced network. The results of the trained models were visualized using the GradCAM and Attention Rollout methods, respectively. First, experiments were conducted on a simple-to-interpret dataset to ensure they were used correctly. The methods are then applied to the set of histological images. In easy-to-understand images (cat images), the convolutional network is more consistent with human perception; on the contrary, in histological images of breast cancer, ViT-B-16 provided results much more similar to the expert's perception.

Importance of higher harmonics and v4 puzzle in quark-gluon plasma tomography

Quark-gluon plasma (QGP) tomography aims to constrain the parameters characterizing the properties and evolution of QGP formed in heavy-ion collisions, by exploiting low- and high-${p}_{\ensuremath{\perp}}$ theory and data. Higher-order harmonics ${v}_{n}$ ($n&gt;2$) are an important---but seldom explored---part of this approach. However, to take full advantage of them, several issues have to be addressed: (i) consistency of different methods for calculating ${v}_{n}$, (ii) importance of event-by-event fluctuations to high-${p}_{\ensuremath{\perp}}\phantom{\rule{4pt}{0ex}}{R}_{AA}$ and ${v}_{2}$ predictions, and (iii) sensitivity of higher harmonics to the initial state of fluid-dynamical evolution. We obtain that (i) several methods for calculating harmonics are compatible with each other, (ii) event-by-event calculations are important in mid-central collisions, and (iii) various initializations of the evolution of the medium lead to quantitatively and qualitatively different predictions, likely to be distinguished by future measurements. We also find that the present high-${p}_{\ensuremath{\perp}}\phantom{\rule{4pt}{0ex}}{v}_{4}$ data cannot be reproduced using initial states for fluid-dynamical evolution given by state-of-the-art models. We call this discrepancy the high-${p}_{\ensuremath{\perp}}{v}_{4}$ puzzle at the Large Hadron Collider.

Differences between joint-space and musculoskeletal estimations of metabolic rate time profiles.

Motion capture laboratories can measure multiple variables at high frame rates, but we can only measure the average metabolic rate of a stride using respiratory measurements. Biomechanical simulations with equations for calculating metabolic rate can estimate the time profile of metabolic rate within the stride cycle. A variety of methods and metabolic equations have been proposed, including metabolic time profile estimations based on joint parameters. It is unclear whether differences in estimations are due to differences in experimental data or due to methodological differences. This study aimed to compare two methods for estimating the time profile of metabolic rate, within a single dataset. Knowledge about the consistency of different methods could be useful for applications such as detecting which part of the gait cycle causes increased metabolic cost in patients. Here we compare estimations of metabolic rate time profiles using a musculoskeletal and a joint-space method. The musculoskeletal method was driven by kinematics and electromyography data and used muscle metabolic rate equations, whereas the joint-space method used metabolic rate equations based on joint parameters. Both estimations of changes in stride average metabolic rate correlated significantly with large changes in indirect calorimetry from walking on different grades showing that both methods accurately track changes. However, estimations of changes in stride average metabolic rate did not correlate significantly with more subtle changes in indirect calorimetry due to walking with different shoe inclinations, and both the musculoskeletal and joint-space time profile estimations did not correlate significantly with each other except in the most downward shoe inclination. Estimations of the relative cost of stance and swing matched well with previous simulations with similar methods and estimations from experimental perturbations. Rich experimental datasets could further advance time profile estimations. This knowledge could be useful to develop therapies and assistive devices that target the least metabolically economic part of the gait cycle.

On the consistency of different methods for detecting aldosterone concentration in blood

Objective To evaluate the consistency of different methods for detecting aldosterone concentration in blood and to establish a reference interval of serum aldosterone concentration by liquid chromatography-tandem mass spectrometry(LC-MS/MS). Methods Concentrations of blood aldosterone were measured by LC-MS/MS, chemiluminescent assays (Diasorin, Domestic A and B systems) and radioimmunoassay (RIA) in 138 healthy adults, 67 patients with essential hypertension and 23 patients with primary aldosteronism. Results Aldosterone concentrations measured by various methods were quiet different(P 0.05) between CLIA(Domestic B) and LC-MS/MS, 0.338(P<0.01) as well as between RIA and LC-MS/MS. Bland-Altman analysis for the measurements showed poor consistency among methods for aldosterone concentrations. The reference interval was 15.2-222.2 pg/ml for serum aldosterone concentrations by LC-MS/MS. Conclusions There are significant differences of blood aldosterone concentrations determined by different methods. Clinically, a specified reference interval might be needed while using different methods. Key words: Aldosterone; Liquid chromatography-tandem mass spectrometry; Chemiluminescent assays; Radioimmunoassay

Acid Ammonium Citrate as P Extractor for Fertilizers of Varying Solubility

ABSTRACT: There are several globally accepted methods to chemically characterize P-fertilizers, but not all are suitable to predict the agronomic efficiency of the P sources in terms of plant nutrition. Our aim was to investigate the performance of P extractors for fertilizers, investigating the consistency of different methods for P sources of varying properties and the related plant responses. The experiment was carried out in a greenhouse, using corn as a model plant. Phosphorus values extractable in water, 2 % citric acid, 2 % formic acid, ammonium neutral citrate + water, and acid ammonium citrate were evaluated for eight P fertilizers of varied solubility and correlated with P uptake by corn. The extractors citric acid and formic acid recovered no predictive amounts of P from crystalline apatite sources (Araxa and Patos phosphate rocks, PRs). However, they showed a satisfactory performance for Bayovar PR and partially acidulated PRs but extracted low amounts of P from soluble P sources such as superphosphates. Neutral ammonium citrate + water extractors could accurately predict the efficiency of soluble P sources but underestimated the performance of Bayovar (a reactive PR). In contrast, the extractor acid ammonium citrate, AAC, (pH 3) accurately predicted the agronomic efficiency of all P fertilizers. We therefore suggest AAC as an effective predictor of the agronomic effectiveness of any inorganic phosphorus sources.

Yapı Analizinde Kullanılan Farklı Yöntemlerin Tutarlılığı Üzerine Bir Çalışma

Yapı Analizinde Kullanılan Farklı Yöntemlerin Tutarlılığı Üzerine Bir Çalışma

English

Different waterlogging tolerance indices between 15 rapeseed (Brassica napus L.) cultivar materials were investigated after seed germinating and field waterlogging, in order to research the consistency of different methods, as well as the effects of waterlogging on yields. The results showed significant variation between the 15 materials. Anoxic germination under room condition resulted in great differences in kinds of waterlogging tolerant indexes, such as vigor index, survival rate, relative seedling length, relative root length and fresh weight; in the fields, plant growths were repressed seriously under waterlogging stress: root fresh weight, root length, aerial parts fresh weight, plant height, plant fresh weight, aerial parts dry weight, root dry weight and root/shoot ratio were decreased by various degrees. Meanwhile, physiological indicators like contents of soluble sugar, soluble protein, malondialdehyde (MDA) and proline, as well as activity of superoxidase (SOD) increased; on the other hand, plant height, number of effective branches, number of pods per plant, number of seeds per pod, yield per plant decreased significantly. Especially, the number of effective branches decreased by 31.81%~78.02% compared with control. 1000-seed weights were increased in some materials. Waterlogging tolerance capabilities varied between materials, but generally, waterlogging tolerant plants showed less genotype reduction. Correlation analysis showed that waterlogging tolerant indices of germinating seed in the room were significantly correlative to those physiological and morphological data in the fields, as well as the final yield characters. Unit conductivity was found significantly negatively correlated with yield per plant, while the relative vigor index was significantly positively correlated with yield per plant. This consistency demonstrated that different methods of determining waterlogging tolerance in rapeseed have the same conclusion. Moreover, it helps predicting the waterlogging tolerance of rapeseed cultivars in the lab conditions so that the breeding of the waterlogging tolerant cultivars can be accelerated in the future. © 2016 Friends Science Publishers

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms.

Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.

A comparison of different methods of Young’s modulus determination for single-wall carbon nanotubes (SWCNT) using molecular dynamics (MD) simulations

The computed values of Young’s modulus ( Y) of single-wall carbon nanotubes given by four common methods based on (i) the determination of stress for a fixed value of strain, (ii) the determination of strain energy for a fixed value of strain, (iii) the longitudinal vibrations, and (iv) the transverse vibrations, and a new method (v) based on the determination of strain for a fixed value of stress have been compared to check the consistency of different methods. The computed values of Y are found to be in agreement with each other with the exception that results of the transverse vibration method differ from those given by other methods when the aspect ratio, namely, the ratio of length to the radius of the tube, is small; the results of the transverse vibration method for the tubes of small diameter are also found to differ from those given by other methods when the commonly used value of thickness of the tube, 3.4 Å, is assumed. The solutions of these problems are discussed in terms of an appropriate consideration for the value of thickness and diameter dependent end-correction in the length of the tube. Effect of defects in the form of vacancies, van der Waals (VDW) interactions, chirality, and diameter of the carbon nanotubes on Y has also been investigated. Y is found to be sensitive to the number of vacancies. Y is found to decrease by ∼1% when VDW interactions between carbon atoms are ignored. Y is also found to be lower for an armchair tube compared to a zigzag tube of the same diameter. As regards the dependence of Y on diameter, we found that as the diameter increases from ∼7 Å to ∼25 Å, Young’s modulus drops by 4% and 8%, respectively, for armchair and zigzag tubes. These results are discussed and compared with other experimental and computed results reported in the literature.

Melanism and Selective Predation in three Species of Moths

In large-scale mark/release/recapture experiments with the polymorphic moth Biston betularia (L.), Kettlewell (1955a, 1956) convincingly demonstrated that birds were taking a disproportionate number of the form which was most conspicuous on the predominant backgrounds at different sites. Differential elimination of the morphs of B. betularia also occurred in experiments in which dead, frozen moths were exposed to predation on trees (Clarke & Sheppard 1966; Bishop 1972; Lees & Creed 1975). Bishop (1972) and Lees & Creed (1975) both found situations in which the melanic form, carbonaria, was present at a high frequency, even though it was at a cryptic disadvantage, relative to the typical form. This is consistent with Ford's (1937, 1975) suggestions that melanic polymorphism in moth species which rely on crypsis depends upon the balance between the selective advantages of both the non-visual and visual attributes controlled by the melanic genes. The results of Bishop (1972) and of Lees & Creed (1975) emphasize the need to estimate selective predation at a number of sites in order to examine the relative importance of non-visual and visual components of selection for different species. Lees, Creed & Duckett (1973) and Bishop et al. (1975) compared melanic frequencies with epiphyte cover (in addition to other variables) at a number of sites. Bishop et al. (1975) have emphasized the difficulties in deducing, from such analyses, whether non-visual or visual selective factors are more likely to be influencing melanic frequency. This can only be done by making more direct estimates of the selective predation of the morphs at different sites. Although predation experiments and mark/release experiments have been carried out with B. betularia at a number of sites, the time and resources required limits the number of sites that can be investigated during the flight period of the moth. However, Kettlewell (1955a, 1956) showed that the conspicuousness of the melanic and typical morphs of B. betularia to humans and to natural predators (birds) were related. Further confirmation of this was obtained by Lees & Creed (1975). The field experiments, described in this paper, were carried out to compare the consistency of different methods of estimating selective predation of the morphs. The work was undertaken in connection with surveys of the relative crypsis of the melanic and typical morphs of three species in southern Britain.