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Optimal invariant sets for atomistic machine learning
The representation of atomic configurations for machine learning models has led to numerous sets of descriptors. However, many descriptor sets are incomplete and/or functionally dependent. Incomplete sets cannot faithfully represent atomic environments. Yet complete constructions often suffer from a high degree of functional dependence, where some descriptors are functions of others. These redundant descriptors do not improve discrimination between atomic environments. We employ pattern recognition techniques to remove dependent descriptors to produce the smallest possible set that satisfies completeness. We apply this in two ways: First, we refine an existing description, the atomic cluster expansion. Second, we augment an incomplete construction, yielding a new message-passing neural network architecture that can recognize up to 5-body patterns. This architecture shows strong accuracy on state-of-the-art benchmarks while retaining low computational cost. Our results demonstrate the utility of this strategy to optimize descriptor sets across a range of descriptors and application datasets.
Transcriptional activation of EGFR by HOXB5 and its role in breast cancer cell invasion
Highlights: • HOXB5 regulates EGFR expression at the transcriptional level. • HOXB5-induced EGFR leads to propagation of downstream signal. • HOXB5-driven invasiveness is largely dependent on EGFR up-regulation. • High co-expression of HOXB5 and EGFR show poor prognosis. HOX genes are transcription factors that play important roles in body patterning and many cellular processes during embryonic, fetal, and adult development. Given their important function in normal tissues, it is reasonable to assume that abnormal expression of HOX genes in adults could lead to serious diseases such as cancer. Our previous study reported HOXB5 to be significantly up-regulated in breast cancer, and its expression was found to be associated with tumor cell proliferation and invasion. Furthermore, the epidermal growth factor receptor (EGFR), a cellular tyrosine kinase that plays an important role in breast cancer progression, was found significantly up-regulated by HOXB5 in ER-positive breast cancer cells. In the present study, we demonstrated that HOXB5 regulates EGFR expression at the transcriptional level by directly binding to its promoter region and promotes phosphorylation of EGFR as well as its downstream effectors. Patients with ER-positive breast cancer, having high co-expression of HOXB5 and EGFR, had poor prognosis than those with low expression. Knockdown studies validated a key role played by EGFR in the HOXB5-induced invasion of breast cancer cells. These results suggest that targeting EGFR could be an effective strategy to treat breast cancer in patients with high HOXB5 expression.
Corexit-EC9527A Disrupts Retinol Signaling and Neuronal Differentiation in P19 Embryonal Pluripotent Cells
Corexit-EC9500A and Corexit-EC9527A are two chemical dispersants that have been used to remediate the impact of the 2010 Deepwater Horizon oil spill. Both dispersants are composed primarily of organic solvents and surfactants and act by emulsifying the crude oil to facilitate biodegradation. The potential adverse effect of the Corexit chemicals on mammalian embryonic development remains largely unknown. Retinol (vitamin A) signaling, mediated by all-trans retinoic acid (RA), is essential for neural tube formation and the development of many organs in the embryo. The physiological levels of RA in cells and tissues are maintained by the retinol signaling pathway (RSP), which controls the biosynthesis of RA from dietary retinol and the catabolism of RA to polar metabolites for removal. RA is a potent activating ligand for the RAR/RXR nuclear receptors. Through RA and the receptors, the RSP modulates the expression of many developmental genes; interference with the RSP is potentially teratogenic. In this study the mouse P19 embryonal pluripotent cell, which contains a functional RSP, was used to evaluate the effects of the Corexit dispersants on retinol signaling and associated neuronal differentiation. The results showed that Corexit-EC9500A was more cytotoxic than Corexit-EC9527A to P19 cells. At non-cytotoxic doses, Corexit-EC9527A inhibited retinol-induced expression of the Hoxa1 gene, which encodes a transcription factor for the regulation of body patterning in the embryo. Such inhibition was seen in the retinol- and retinal- induced, but not RA-induced, Hoxa1 up-regulation, indicating that the Corexit chemicals primarily inhibit RA biosynthesis from retinal. In addition, Corexit-EC9527A suppressed retinol-induced P19 cell differentiation into neuronal cells, indicating potential neurotoxic effect of the chemicals under the tested conditions. In conclusion, the surfactant ingredient, dioctyl sodium sulfosuccinate (DOSS), may be a major contributor to the observed effect of Corexit-EC9527A in the cell.
Histologic Subtype in Core Lung Biopsies of Early-Stage Lung Adenocarcinoma is a Prognostic Factor for Treatment Response and Failure Patterns After Stereotactic Body Radiation Therapy
Purpose: Stereotactic body radiation therapy (SBRT) has emerged as an effective treatment for early-stage lung cancer. The histologic subtype of surgically resected lung adenocarcinoma is recognized as a prognostic factor, with the presence of solid or micropapillary patterns predicting poor outcomes. We describe the outcomes after SBRT for early-stage lung adenocarcinoma stratified by histologic subtype. Methods and Materials: We identified 119 consecutive patients (124 lesions) with stage I to IIA lung adenocarcinoma who had undergone definitive SBRT at our institution from August 2008 to August 2015 and had undergone core biopsy. Histologic subtyping was performed according to the 2015 World Health Organization classification. Of the 124 tumors, 37 (30%) were a high-risk subtype, defined as containing a component of solid and/or micropapillary pattern. The cumulative incidences of local, nodal, regional, and distant failure were compared between the high-risk and non–high-risk adenocarcinoma subtypes using Gray's test, and multivariable-adjusted hazard ratios (HRs) were estimated from propensity score–weighted Cox regression models. Results: The median follow-up for the entire cohort was 17 months and for surviving patients was 21 months. The 1-year cumulative incidence of and adjusted HR for local, nodal, regional, and distant failure in high-risk versus non–high-risk lesions was 7.3% versus 2.7% (HR 16.8; 95% confidence interval [CI] 3.5-81.4), 14.8% versus 2.6% (HR 3.8; 95% CI 0.95-15.0), 4.0% versus 1.2% (HR 20.9; 95% CI 2.3-192.3), and 22.7% versus 3.6% (HR 6.9; 95% CI 2.2-21.1), respectively. No significant difference was seen with regard to overall survival. Conclusions: The outcomes after SBRT for early-stage adenocarcinoma of the lung correlate highly with histologic subtype, with micropapillary and solid tumors portending significantly higher rates of locoregional and metastatic progression. In this context, the histologic subtype determined from core biopsies is a prognostic factor and could have important implications for patient selection, adjuvant treatment, biopsy methods, and clinical trial design.
Practice Patterns of Pediatric Total Body Irradiation Techniques: A Children's Oncology Group Survey
The aim of this study was to examine current practice patterns in pediatric total body irradiation (TBI) techniques among COG member institutions.
Male body size predicts reproductive success but not within-clutch paternity patterns in gopher tortoises ( Gopherus polyphemus )
In many vertebrates, body size is an important driver of variation in male reproductive success. Larger, more fit individuals are more likely to dominate mating opportunities, skewing siring success and resulting in lower effective population sizes and genetic diversity. The mating system of the gopher tortoise (Gopherus polyphemus) has been characterized as both female defense and scramble-competition polygyny. Mating systems are typically not fixed and can be influenced by factors such as population density, demographic structure, and environmental conditions;, however, most populations will have a predominant strategy that results from local conditions. We assessed how male body size influences patterns of paternity and reproductive success in a natural population of gopher tortoises in Florida, USA. Using microsatellites, we assigned parentage of 220 hatchlings from 31 nests collected during two reproductive seasons. Larger males were significantly more likely to sire offspring and sired more offspring than smaller males; however, the likelihood of a clutch being multiply-sired was unrelated to male body size. We also found evidence of mate fidelity across years. Although paternity patterns in this high-density population are more consistent with defense polygyny, female monopoly by males was incomplete, with both large and small males contributing to multiply-sired clutches. Additional behavioral data are needed to clarify the role of female mate selection in paternity outcomes. The context-dependence of mating systems underscores the need to compare parentage patterns across populations and to recognize the potential for more than one strategy to be employed within a single population.
Imaging post-stereotactic body radiation therapy responses for hepatocellular carcinoma: typical imaging patterns and pitfalls
Stereotactic body radiation therapy (SBRT) has increased utility in the management of hepatocellular carcinoma (HCC) ranging from local therapy in early-stage HCC not suitable for other focal therapies to end-stage HCC. As the indications for the use of SBRT in HCC expand, diagnostic imaging is being increasingly used to assess response to treatment. The imaging features of tumor response do not parallel those of other focal therapies such as radiofrequency ablation or trans-arterial chemoembolization that immediately devascularize the tumor. The tumor response to SBRT on imaging takes much longer and often shows gradual changes including the reduction of enhancement and size over several months. It is essential to recognize the typical imaging patterns of response, as well as the appearance of focal liver reaction in the non-target liver that can confound image interpretation. The timing of treatment response assessment imaging is fundamental to minimize the potential for false negative response. The purpose of this article is to review the variable post-SBRT imaging features of HCC and adjacent liver parenchyma and discuss the potential pitfalls of imaging evaluation after SBRT for HCC.
Symmetry breaking in the body-fixed electron emission pattern due to electron-retroaction in the photodissociation of H 2 + and D 2 + close to threshold
Not Available
Stabilization of green bodies via sacrificial gelling agent during electrophoretic deposition
In one embodiment, a method for electrophoretic deposition of a three-dimensionally patterned green body includes suspending a first material in a gelling agent above a patterned electrode of an electrophoretic deposition (EPD) chamber, and gelling the suspension while applying a first electric field to the suspension to cause desired patterning of the first material in a resulting gelation. In another embodiment, a ceramic, metal, or cermet includes a plurality of layers, wherein each layer includes a gradient in composition, microstructure, and/or density in an x-y plane oriented parallel to a plane of deposition of the plurality of layers along a predetermined distance in a z-direction perpendicular to the plane of deposition.
Patterns of Intraosseous Recurrence After Stereotactic Body Radiation Therapy for Coxal Bone Metastasis
To analyze the detailed pattern of intraosseous failure after stereotactic body radiation therapy (SBRT) for coxal bone metastasis.
3D printing of void-free glass monoliths: rheological and geometric considerations
Direct ink writing (DIW) is a versatile additive manufacturing technique capable of printing 3D architectures from a broad range of materials. The key advantage of DIW is the ability to spatially control both the architecture and the composition of the printed part, which enables the production of components with previously unachievable combinations of functionalities. One emergent application space for DIW has been in additively manufactured glass optics, where a “green body” is patterned layer-by-layer by extruding a silica-based slurry through a microfluidic nozzle and then thermally consolidated to transparent glass. A critical aspect of the process is ensuring that the printed part is completely free of voids that can occur in the interstitial spaces between the extruded filaments. This outcome is governed by the interplay between ink rheology and strains imposed by the printing process and geometric packing of the filaments. Here, we explore the strain- and rate-dependent deformation events in the DIW process to determine conditions that enable the printing of void-free monoliths without sacrificing shape fidelity. We focus on yield stress fluids consisting of fumed silica nanoparticles dispersed in organic solvents at varied volume fractions to control the rheological properties. We investigate the printability of these ink materials as a function of print process variables and devise the appropriate dimensionless parameters that capture the geometry-dependent and rate-dependent effects on the deformation of the extruded ink. Lastly, we use these scaling arguments to construct a phase diagram for void-free monolith printability.
The N-terminal domain of gastrulation brain homeobox 2 (Gbx2) is required for iridophore specification in zebrafish
Highlights: • Iridophore formation is suppressed by gbx2 knockdown in zebrafish. • gbx2 is expressed in neural crest cells and iridophores during development. • gbx2 knockdown leads to apoptosis of neural crest cells. • The N-terminal domain of Gbx2 rescues the phenotype of gbx2 knockdown. Although body color pattern formation by pigment cells plays critical roles in animals, pigment cell specification has not yet been fully elucidated. In zebrafish, there are three chromatophores: melanophore, iridophore, and xanthophore, that are derived from neural crest cells (NCCs). A recent study has reported the differentially expressed genes between melanophores and iridophores. Based on transcriptome data, we identified that Gbx2 is required for iridophore specification during development. In support of this, iridophore formation is suppressed by gbx2 knockdown by morpholino antisense oligonucleotide, at 72 h post fertilization (hpf) in zebrafish. Moreover, gbx2 is expressed in sox10-expressing NCCs and guanine crystal plates-containing iridophores during development at 24 and 48 hpf, respectively. In gbx2 knockdown zebrafish embryos, apoptosis of sox10-expressing NCCs was detected at 24 hpf without any effect on the formation of melanophores and xanthophores at 48 hpf. We further observed that the N-terminal domain of Gbx2 is able to rescue the iridophore formation defect caused by gbx2 knockdown. Our study provides insights into the requirement of N-terminal domain of Gbx2 for iridophore specification in zebrafish.
A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival
Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.
Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement
Time-lapse images of cells and tissues contain rich information about dynamic cell behaviours, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here we exploit deep reinforcement learning (DRL) to infer cell–cell interactions and collective cell behaviours in tissue morphogenesis from three-dimensional (3D) time-lapse images. We use hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with a ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to Caenorhabditis elegans embryogenesis, HDRL reveals a multiphase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.
Patterned structures of graphene and graphitic carbon and methods for their manufacture
A patterned graphene or graphitic body is produced by providing a three-dimensionally patterned carbonaceous body; coating the body with a catalytic metal whereby is formed a coating having an inner surface proximal the body and an outer surface distal the body; and annealing the coated body under time and temperature conditions effective to form a graphene or graphitic layer on the outer surface of the catalytic metal coating.
Patterned structures of graphene and graphitic carbon and methods for their manufacture
A patterned graphene or graphitic body is produced by providing a three-dimensionally patterned carbonaceous body; coating the body with a catalytic metal whereby is formed a coating having an inner surface proximal the body and an outer surface distal the body; and annealing the coated body under time and temperature conditions effective to form a graphene or graphitic layer on the outer surface of the catalytic metal coating.
Geographic variation in body size and sexual size dimorphism of North American Ratsnakes ( Pantherophis spp. s.l.)
Because body size affects nearly all facets of an organism’s life history, ecologists have long been interested in large-scale patterns of body-size variation, as well as why those large-scale patterns often differ between sexes. We explored body-size variation across the range of the sexually dimorphic Ratsnake complex (species of the genus Pantherophis Fitzinger, 1843 s.l.; formerly Elaphe obsoleta (Say in James, 1823)) in North America. We specifically explored whether variation in body size followed latitudinal patterns or varied with climatic variables. We found that body size did not conform to a climatic or latitudinal gradient, but instead, some of the populations with the largest snakes occurred near the core of the geographic range and some with the smallest occurred near the northern, western, and southern peripheries of the range. Males averaged 14% larger than females, although the degree of sexual size dimorphism varied between populations (range: 2%–25%). There was a weak trend for male body size to change in relation to temperature, whereas female body size did not. Our results indicate that relationships between climate and an ectotherm’s body size are more complicated than linear latitudinal clines and likely differ for males and females.