The image biomarker standardization initiative: Standardized convolutional filters for reproducible radiomics and enhanced clinical insights

Standardizing convolutional filters that enhance specific structures and patterns in medical imaging enables reproducible radiomics analyses, improving consistency and reliability for enhanced clinical insights. Filters are commonly used to enhance specific structures and patterns in images, such as vessels or peritumoral regions, to enable clinical insights beyond the visible image using radiomics. However, their lack of standardization restricts reproducibility and clinical translation of radiomics decision support tools. In this special report, teams of researchers who developed radiomics software participated in a three-phase study (September 2020 to December 2022) to establish a standardized set of filters. The first two phases focused on finding reference filtered images and reference feature values for commonly used convolutional filters: mean, Laplacian of Gaussian, Laws and Gabor kernels, separable and nonseparable wavelets (including decomposed forms), and Riesz transformations. In the first phase, 15 teams used digital phantoms to establish 33 reference filtered images of 36 filter configurations. In phase 2, 11 teams used a chest CT image to derive reference values for 323 of 396 features computed from filtered images using 22 filter and image processing configurations. Reference filtered images and feature values for Riesz transformations were not established. Reproducibility of standardized convolutional filters was validated on a public data set of multimodal imaging (CT, fluorodeoxyglucose PET, and T1-weighted MRI) in 51 patients with soft-tissue sarcoma. At validation, reproducibility of 486 features computed from filtered images using nine configurations × three imaging modalities was assessed using the lower bounds of 95% CIs of intraclass correlation coefficients. Out of 486 features, 458 were found to be reproducible across nine teams with lower bounds of 95% CIs of intraclass correlation coefficients greater than 0.75. In conclusion, eight filter types were standardized with reference filtered images and reference feature values for verifying and calibrating radiomics software packages. A web-based tool is available for compliance checking

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum.

Many bacteria move using a complex, self-assembling nanomachine, the bacterial flagellum. Biosynthesis of the flagellum depends on a flagellar-specific type III secretion system (T3SS), a protein export machine homologous to the export machinery of the virulence-associated injectisome. Six cytoplasmic (FliH/I/J/G/M/N) and seven integral-membrane proteins (FlhA/B FliF/O/P/Q/R) form the flagellar basal body and are involved in the transport of flagellar building blocks across the inner membrane in a proton motive force-dependent manner. However, how the large, multi-component transmembrane export gate complex assembles in a coordinated manner remains enigmatic. Specific for most flagellar T3SSs is the presence of FliO, a small bitopic membrane protein with a large cytoplasmic domain. The function of FliO is unknown, but homologs of FliO are found in >80% of all flagellated bacteria. Here, we demonstrate that FliO protects FliP from proteolytic degradation and promotes the formation of a stable FliP-FliR complex required for the assembly of a functional core export apparatus. We further reveal the subcellular localization of FliO by super-resolution microscopy and show that FliO is not part of the assembled flagellar basal body. In summary, our results suggest that FliO functions as a novel, flagellar T3SS-specific chaperone, which facilitates quality control and productive assembly of the core T3SS export machinery

The Sweaty 2017 RoboCup Humanoid Adult Size Team Description

This paper describes the Sweaty II humanoid adult size robot trying to qualify for the RoboCup 2017 adult size humanoid competition. Sweaty came 2nd in RoboCup 2016 adult size league. The paper describes the main characteristics of Sweaty that made this success possible, and improvements that have been made or are planned to be implemented for RoboCup 2017

Expression of Ano1 and Ca²⁺ activated Cl⁻ currents in HNSCC cells.

<p>A) Western blots of Ano1 expressed in the three different human cell lines CAL-27, CAL-33, and BHY. B) Current/voltage relationships of whole cell currents activated by 100 µM ATP (filled circles) in CAL-27, CAL-33, and BHY cells. Application of the K⁺ channel inhibitors Ba²⁺ (5 mM) and TEA⁺ (10 mM) (grey circles) did not significantly change currents, suggesting a dominant role Cl⁻ currents. C) Summary of the calculated ATP-activated whole cell conductances. Mean ± SEM, (number of experiments).</p

Analysis of the 11q13 (Ano1 and CCND1) genomic amplification and protein expression in 365 HNSCCs.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043265#pone-0043265-t001" target="_blank"><b>Table 1</b></a><b> Legend.</b> A) Overview of the prevalence of genomic amplification of <i>Ano1</i> and Ano1 expression in HNSCCs from different tumor locations.</p><p>B)Genomic amplification of the 11q13 locus is associated with the presence of Ano1 protein expression.</p><p>C)Strong correlation between the genomic amplification of <i>Ano1</i> and <i>CCND1</i>.</p

<i>Ano1 causes cell migration.</i>

<p>A) Summary of BrdU incorporation in BHY cells after various treatments, shown as % of BrdU incorporation, when compared to cells treated with scrambled RNA (red dashed line). B) Representative images of wound healing in a scratch assay with BHY cells, treated with scrambled RNA (upper panels) or after Ano1-knockdown with siRNA-Ano1 (lower panels). Yellow arrowheads indicate edges of the damage. C) Time course for the wound healing process (closure of the scratch) for control cells (scrambled RNA) and after Ano1-knockdown (si-Ano1). D) Migration of BHY and CAL-33 cells measured continuously as cell index using the xCELLigence system. Inhibition of migration by blockade of Ano1 with AO1 (10 µM). E) Cell Proliferation measured continuously as cell index using the xCELLigence system. AO1 (10 µM) has no effect on proliferation. Experiments were performed at least in triplicates. Mean ± SEM, (number of experiments). ^#indicates significant difference (p<0.05, ANOVA).</p

Comprehensive analysis of Ano1 protein expression in normal tissues.

<p>#Mucosa and mucous glands were negative.</p><p>Summary of normal tissues with detectable Ano1 protein expression. Most normal tissues do not express Ano1. Only gall bladder, stomach and duodenum express Ano1 (A). Apical positivity (B) and Ano1-positive Cajal cells (C) were detected in several types of tissues. (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043265#pone.0043265.s005" target="_blank">Table S5</a> for complete listing.).</p