Extent of Coverage; Liabilities of Limited Coverage

Author(s):  
David Upton
Keyword(s):  
2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jingjie Shang ◽  
Zhiqiang Tan ◽  
Yong Cheng ◽  
Yongjin Tang ◽  
Bin Guo ◽  
...  

Abstract Background Standardized uptake value (SUV) normalized by lean body mass ([LBM] SUL) is recommended as metric by PERCIST 1.0. The James predictive equation (PE) is a frequently used formula for LBM estimation, but may cause substantial error for an individual. The purpose of this study was to introduce a novel and reliable method for estimating LBM by limited-coverage (LC) CT images from PET/CT examinations and test its validity, then to analyse whether SUV normalised by LC-based LBM could change the PERCIST 1.0 response classifications, based on LBM estimated by the James PE. Methods First, 199 patients who received whole-body PET/CT examinations were retrospectively retrieved. A patient-specific LBM equation was developed based on the relationship between LC fat volumes (FVLC) and whole-body fat mass (FMWB). This equation was cross-validated with an independent sample of 97 patients who also received whole-body PET/CT examinations. Its results were compared with the measurement of LBM from whole-body CT (reference standard) and the results of the James PE. Then, 241 patients with solid tumours who underwent PET/CT examinations before and after treatment were retrospectively retrieved. The treatment responses were evaluated according to the PE-based and LC-based PERCIST 1.0. Concordance between them was assessed using Cohen’s κ coefficient and Wilcoxon’s signed-ranks test. The impact of differing LBM algorithms on PERCIST 1.0 classification was evaluated. Results The FVLC were significantly correlated with the FMWB (r=0.977). Furthermore, the results of LBM measurement evaluated with LC images were much closer to the reference standard than those obtained by the James PE. The PE-based and LC-based PERCIST 1.0 classifications were discordant in 27 patients (11.2%; κ = 0.823, P=0.837). These discordant patients’ percentage changes of peak SUL (SULpeak) were all in the interval above or below 10% from the threshold (±30%), accounting for 43.5% (27/62) of total patients in this region. The degree of variability is related to changes in LBM before and after treatment. Conclusions LBM algorithm-dependent variability in PERCIST 1.0 classification is a notable issue. SUV normalised by LC-based LBM could change PERCIST 1.0 response classifications based on LBM estimated by the James PE, especially for patients with a percentage variation of SULpeak close to the threshold.


PEDIATRICS ◽  
1969 ◽  
Vol 44 (3) ◽  
pp. 452-452
Author(s):  
Deryle T. Whipple

In a recent article in Pediatrics (43:290, 1969) , Dr. Cone reviewed the approach to a child with fever. The list of patients with fever of undetermined origin will shrink markedly in the presence of a complete physical examination (especially the ears), a CBC, and urinalysis performed properly. I am surprised Dr. Cone omits infectious mononucleosis from his admittedly limited coverage of this subject. In the young child the Mono test or Heterophile may remain consistently normal.


2018 ◽  
Vol 115 (50) ◽  
pp. 12769-12774 ◽  
Author(s):  
Roseina Woods ◽  
Samuel T. Turvey ◽  
Selina Brace ◽  
Ross D. E. MacPhee ◽  
Ian Barnes

The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori. We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus. These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5–18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.


2014 ◽  
Vol 48 (3) ◽  
pp. 104-114 ◽  
Author(s):  
Yoshiki Sato ◽  
Toshihiro Maki ◽  
Ayaka Kume ◽  
Takumi Matsuda ◽  
Takashi Sakamaki ◽  
...  

AbstractAutonomous underwater vehicles (AUVs) can operate without the need for human control or tether cables as long as there is sufficient energy. AUVs have recently been used for seafloor imaging. Visual observation by AUVs provides high-resolution color information of the seafloor. However, conventional observation techniques that follow a prespecified path offer limited coverage because it is impossible for operators to build a suitable path in unknown rough terrain. A flawed prespecified path will produce incomplete observation. If unobserved areas are found during postprocessing, another dive is necessary, which increases the total cost. To overcome this problem, the authors have proposed a path replanning method to realize high-coverage observation in one dive. With this method, the AUV evaluates unobserved areas after the first prespecified observation; if unobserved areas are found, the AUV recreates an appropriate path to cover what was missed. The validity of the proposed method was previously evaluated using an artificial target in a tank and in shallow seas at a depth of approximately 35 m. In this study, the feasibility of the method was validated in a more challenging setting: experimental data were taken from a hydrothermal vent field in Kagoshima Bay, Japan.


2019 ◽  
Vol 3 (2) ◽  
pp. 61-71 ◽  
Author(s):  
Gunnar Sivertsen

Abstract Internationalization is important for research quality and for specialization on new themes in the social sciences and humanities (SSH). Interaction with society, however, is just as important in these areas of research for realizing the ultimate aims of knowledge creation. This article demonstrates how the heterogenous publishing patterns of the SSH may reflect and fulfill both purposes. The limited coverage of the SSH in Scopus and Web of Science is discussed along with ideas about how to achieve a more complete representation of all the languages and publication types that are actually used in the SSH. A dynamic and empirical concept of balanced multilingualism is introduced to support combined strategies for internationalization and societal interaction. The argument is that all the communication purposes in all different areas of research, and all the languages and publication types needed to fulfill these purposes, should be considered in a holistic manner without exclusions or priorities whenever research in the SSH is evaluated.


2020 ◽  
Vol 495 (3) ◽  
pp. 3124-3159 ◽  
Author(s):  
Ryley Hill ◽  
Scott Chapman ◽  
Douglas Scott ◽  
Yordanka Apostolovski ◽  
Manuel Aravena ◽  
...  

ABSTRACT We present an extensive ALMA spectroscopic follow-up programme of the $z\, {=}\, 4.3$ structure SPT2349–56, one of the most actively star-forming protocluster cores known, to identify additional members using their [C ii] 158 μm and CO(4–3) lines. In addition to robustly detecting the 14 previously published galaxies in this structure, we identify a further 15 associated galaxies at $z\, {=}\, 4.3$, resolving 55$\, {\pm }\,$5 per cent of the 870 μm flux density at 0.5 arcsec resolution compared to 21 arcsec single-dish data. These galaxies are distributed into a central core containing 23 galaxies extending out to 300 kpc in diameter, and a northern extension, offset from the core by 400 kpc, containing three galaxies. We discovered three additional galaxies in a red Herschel-SPIRE source 1.5 Mpc from the main structure, suggesting the existence of many other sources at the same redshift as SPT2349–56 that are not yet detected in the limited coverage of our data. An analysis of the velocity distribution of the central galaxies indicates that this region may be virialized with a mass of (9$\pm 5)\, {\times }\, 10^{12}$  M⊙, while the two offset galaxy groups are about 30 and 60 per cent less massive and show significant velocity offsets from the central group. We calculate the [C ii] and far-infrared number counts, and find evidence for a break in the [C ii] luminosity function. We estimate the average SFR density within the region of SPT2349–56 containing single-dish emission (a proper diameter of 720 kpc), assuming spherical symmetry, to be roughly 4$\, {\times }\, 10^4$ M⊙ yr−1 Mpc−3; this may be an order of magnitude greater than the most extreme examples seen in simulations.


Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 587-614 ◽  
Author(s):  
Gabriel Renaud ◽  
Kristian Hanghøj ◽  
Thorfinn Sand Korneliussen ◽  
Eske Willerslev ◽  
Ludovic Orlando

Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5–6× and down to 7–8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.


2019 ◽  
Vol 35 (14) ◽  
pp. i305-i314 ◽  
Author(s):  
Muhao Chen ◽  
Chelsea J -T Ju ◽  
Guangyu Zhou ◽  
Xuelu Chen ◽  
Tianran Zhang ◽  
...  

AbstractMotivationSequence-based protein–protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information.ResultsWe present an end-to-end framework, PIPR (Protein–Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short.Availability and implementationThe implementation is available at https://github.com/muhaochen/seq_ppi.git.Supplementary informationSupplementary data are available at Bioinformatics online.


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