Optimization of Traced Neuron Skeleton Using Lasso-Based Model

Reconstruction of neuronal morphology from images involves mainly the extraction of neuronal skeleton points. It is an indispensable step in the quantitative analysis of neurons. Due to the complex morphology of neurons, many widely used tracing methods have difficulties in accurately acquiring skeleton points near branch points or in structures with tortuosity. Here, we propose two models to solve these problems. One is based on an L1-norm minimization model, which can better identify tortuous structure, namely, a local structure with large curvature skeleton points; the other detects an optimized branch point by considering the combination patterns of all neurites that link to this point. We combined these two models to achieve optimized skeleton detection for a neuron. We validate our models in various datasets including MOST and BigNeuron. In addition, we demonstrate that our method can optimize the traced skeletons from large-scale images. These characteristics of our approach indicate that it can reduce manual editing of traced skeletons and help to accelerate the accurate reconstruction of neuronal morphology.

Abstract P6-07-02: The CARMA3-Bcl10-MALT1 signalosome mediates pro-angiogenic IL-6 and IL-8 paracrine signaling in GPCR+ breast cancer

Background: The overexpression of selected G-protein coupled receptors (GPCRs) has been linked to the pathogenesis of multiple cancer subtypes. We recently demonstrated that overexpression of two such GPCRs, the angiotensin II receptor type I (AGTR1) and protease-activated receptor type 1 (PAR1), occurs in a substantial fraction of luminal breast cancers and is associated with treatment resistance and poor prognosis. Further, experimental models demonstrate that overexpression of these receptors in breast cancer cell lines promotes aggressive features that include EMT, invasion, migration, and loss of ER expression. In addition to these cell intrinsic effects, we find that GPCR overexpression in breast cancer cells can impact the tumor microenvironment. Specifically, we recently reported that conditioned media from angiotensin II-stimulated AGTR1+ breast cancer cells induces endothelial chemotaxis in vitro and tumor angiogenesis in vivo. We also demonstrated that this pro-angiogenic phenotype requires the CARMA3-Bcl10-MALT1 (CBM) signalosome, a signaling complex that links upstream GPCR stimulation with downstream NF-κB activation. We hypothesized that stimulation of either AGTR1 or PAR1 induces CBM-dependent secretion of NF-κB responsive, pro-angiogenic factors from these GPCR+ breast cancer cells which then exert proangiogenic effects on neighboring endothelial cells through paracrine signaling.

Methods: To identify CBM-dependent secreted factors, we evaluated the AGTR1+ BT549 cell line, +/- Bcl10 or MALT1 siRNA knockdown, for expression of 770 genes of significance to solid tumor pathogenesis using the NanoString PanCancer Progression Panel followed by Ingenuity Pathway Analysis (IPA). RT-PCR and ELISA were used to validate hits and determine if the CBM signalosome controls expression of the same genes in the PAR1+ cell lines, MCF7-N55 and MDA-MB-231.

Results: We identified IL-6 and IL-8 signaling pathways as the two most significantly downregulated angiogenesis pathways following either Bcl10 or MALT1 knockdown. Using quantitative RT-PCR and ELISA, we confirmed that IL-6 and IL-8 gene expression and protein secretion are significantly induced in response to stimulation of BT549 cells by angiotensin II and MCF7-N55 and MDA-MB-231 cells by TRAP6, a PAR1 agonist. siRNA-mediated MALT1 knockdown in BT549 cells led to a significant reduction of IL-6 and IL-8 gene expression upon angiotensin II stimulation; similarly, CRISPR/Cas9-mediated MALT1-deletion in MCF7-N55 cells resulted in failure of these cells to secrete IL-8 upon TRAP6 stimulation.

Conclusions: The GPCR-CBM-cytokine signaling pathway provides a common druggable target to curb pro-angiogenenic paracrine signaling in GPCR+ breast cancers. Importantly, the CBM signalosome has also been shown to be required for IL-8 dependent upregulation of VEGF in endothelial cells, indicating that inhibition of the signalosome could exert complementary effects on both cancer cells and endothelial cells to effectively limit the pro-angiogenic phenotype driven by GPCR overexpression. Several small-molecule MALT1 inhibitors are now available and can be tested for their efficacy as angiogenesis inhibitors in the setting of GPCR+ breast cancer.

Citation Format: Kang H, Ekambaram P, McAllister-Lucas LM, Lucas PC. The CARMA3-Bcl10-MALT1 signalosome mediates pro-angiogenic IL-6 and IL-8 paracrine signaling in GPCR+ breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-07-02.

Revealing Color Forces with Transverse Polarized Electron Scattering

The Spin Asymmetries of the Nucleon Experiment measured two double spin asymmetries using a polarized proton target and polarized electron beam at two beam energies, 4.7 and 5.9 GeV. A large-acceptance open-configuration detector package identified scattered electrons at 40° and covered a wide range in Bjorken x (0.3<x<0.8). Proportional to an average color Lorentz force, the twist-3 matrix element, d[over ˜]_{2}^{p}, was extracted from the measured asymmetries at Q^{2} values ranging from 2.0 to 6.0  GeV^{2}. The data display the opposite sign compared to most quark models, including the lattice QCD result, and an unexpected scale dependence. Furthermore, when combined with the neutron data in the same Q^{2} range the results suggest a flavor independent average color Lorentz force.

[Active and passive maternal smoking during pregnancy and risk of having a child with polydactyly: a case-control study]

Objective: The number of children with polydactyly is increasing. In addition to genetic factors, an influence of maternal behavior or environmental effects during pregnancy is becoming increasingly apparent. However, epidemiological data on these effects are lacking. Methods: This hospital-based, case-control study enrolled 143 infants with polydactyly and 286 controls without genetic diseases to evaluate the association between active and passive maternal smoking during pregnancy and the likelihood of giving birth to a child with polydactyly. Results: Active and passive maternal smoking during pregnancy was associated with an increased risk of giving birth to a child with polydactyly (active smoking: OR=4.74, 95%CI: 1.43-15.65, P=0.011; passive smoking: OR=2.42, 95%CI: 1.32-4.44, P=0.004). After adjusting for confounders, smoking during pregnancy remained significant influence on polydactyly (active smoking: aOR=7.27, 95%CI: 1.72-30.72, P=0.007; passive smoking: aOR=2.41, 95%CI: 1.11-5.23, P=0.026). Conclusion: Active and passive maternal smoking during pregnancy appears to be a risk factor for polydactyly in newborns.

Monodisperse Cu/Cu2O@C core-shell nanocomposite supported on rGO layers as an efficient catalyst derived from a Cu-based MOF/GO structure

A novel copper/copper(i) oxide@carbon (Cu/Cu2O@C) core-shell nanocomposite monodispersed on the surface of reduced graphene oxide (defined as Cu/Cu2O@C-rGO) was synthesized using a one-step calcination of Cu-based metal organic frameworks (MOFs)/graphene oxide (GO) composite structure. The size of the resultant Cu/Cu2O@C core-shell nanoparticles (NPs) on the rGO layers were mainly distributed in range of about 90-100 nm with good dispersion, which was characterized using transmission electron microscopy. X-ray diffraction, Raman spectroscopy, Fourier transform infrared spectroscopy, nitrogen adsorption-desorption isotherms, X-ray photoelectron spectrometry and thermogravimetric analyses were also carried out to characterize the structure and composition of the Cu/Cu2O@C-rGO. The catalytic performance of the Cu/Cu2O@C-rGO composite was evaluated using a reduction reaction from 4-nitrophenol to 4-aminophenol. It was demonstrated that the Cu/Cu2O@C-rGO composite exhibited an excellent catalytic performance, which can reach a nearly 100% conversion rate in 90 s with 0.1 mg of catalyst. This catalyst also showed a good performance for the degradation of other organic dyes such as methylene blue, methyl orange and rhodamine B. Additionally, the core-shell structure exhibited good stability and reusability for the reduction reaction, which was because of its relatively better oxidation resistance than that of the bare Cu NPs. This research provided an efficient and stable non-noble metal-based catalyst derived from the MOF/GO structure.

Gadolinium Deposition in Deep Brain Structures: Relationship with Dose and Ionization of Linear Gadolinium-Based Contrast Agents

BACKGROUND AND PURPOSE

Dose-dependent association between hyperintensity in deep brain structures on unenhanced T1WIs and gadolinium-based contrast agent administrations has been demonstrated with subsequent histopathological confirmation of gadolinium deposition. Our aim was to determine whether greater exposure to linear gadolinium-based contrast agent administration is associated with higher signal intensity in deep brain structures on unenhanced T1-weighted MR imaging. Secondary objective was to compare signal intensity differences between ionic and nonionic linear gadolinium-based contrast agents.

MATERIALS AND METHODS

Subjects with secondary-progressive MS originally enrolled in a multicenter clinical trial were studied retrospectively. Eighty subjects (high-exposure cohort) received 9 linear gadolinium-based contrast agent administrations (30 nonionic/50 ionic) between week -4 and year 1 and a tenth administration by year 2. One hundred fifteen subjects (low-exposure cohort) received 2 administrations (40 nonionic/75 ionic) between week -4 and year 1 and a third administration by year 2. Signal intensities were measured on unenhanced T1WIs by placing sample-points on the dentate nucleus, globus pallidus, caudate, thalamus, pons, and white matter, and they were normalized using the following ratios: dentate/pons, globus pallidus/white matter, caudate/white matter, and thalamus/white matter.

RESULTS

Between week -4 and year 1, subjects in the high-exposure cohort showed increased signal intensity ratios in all regions (P < .01), while the low-exposure cohort showed only an increase in the dentate nucleus (P = .003). Between years 1 and 2, when both cohorts received only 1 additional gadolinium-based contrast agent, no significant changes were observed. In the high-exposure cohort, significantly higher changes in signal intensity ratios were observed in subjects receiving linear nonionic than in those receiving linear ionic gadolinium-based contrast agents.

CONCLUSIONS

Hyperintensity in deep brain structures from gadolinium deposition is related to the number of doses and the type of linear gadolinium-based contrast agent (nonionic greater than ionic) administration.

Nut-like MOF/hydroxylated graphene hybrid materials for adsorptive desulfurization of thiophene

Nowadays, sulfur compounds in fuel oils are the main source of environmental pollution and ultra-deep desulfurization of fuel oils has become a top priority. Many porous materials such as activated carbon and metal-organic frameworks (MOFs) have attracted attention in the field of adsorption desulfurization in recent years. A series of novel MOF/hydroxylated graphene hybrid materials were successfully designed and synthesized with different ratios for application in the field of ADS. The hydroxylated graphene (HG) was found dispersed not just on the surface but also inserted in the MOF crystals in what we call a nut-like structure. It was found that the introduction of a small amount (<8%) of HG does not hinder the formation of the Cu-BTC structure. Meanwhile, the adsorption performances of these composites for thiophene from oils were evaluated using batch adsorption tests at room temperature. The synergistic effect between Cu-BTC and HG in the hybrid materials can improve the adsorption capacity for thiophene molecules. The experimental equilibrium curve fitted well with the theoretical Langmuir isotherm model. The maximum sulfur adsorption capacity of 35.6 mg S g-1 for the hybrid materials was calculated using the Langmuir adsorption equation, which increased by 48% compared to parent Cu-BTC. Thus, these hybrid materials have great potential for application in the adsorptive desulfurization process, especially for thiophenic compounds.

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Background

Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis.

Patients and methods

We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes.

Results

Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016).

Conclusions

Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Timing Recollision in Nonsequential Double Ionization by Intense Elliptically Polarized Laser Pulses

We examine correlated electron and doubly charged ion momentum spectra from strong field double ionization of neon employing intense elliptically polarized laser pulses. An ellipticity-dependent asymmetry of correlated electron and ion momentum distributions has been observed. Using a 3D semiclassical model, we demonstrate that our observations reflect the subcycle dynamics of the recollision process. Our Letter reveals a general physical picture for recollision impact double ionization with elliptical polarization and demonstrates the possibility of ultrafast control of the recollision dynamics.

In vitro bioassessment of the immunomodulatory activity of Saccharomyces cerevisiae components using bovine macrophages and Mycobacterium avium ssp. paratuberculosis

The yeast Saccharomyces cerevisiae and its components are used for the prevention and treatment of enteric disease in different species; therefore, they may also be useful for preventing Johne's disease, a chronic inflammatory bowel disease of ruminants caused by Mycobacterium avium ssp. paratuberculosis (MAP). The objective of this study was to identify potential immunomodulatory S. cerevisiae components using a bovine macrophage cell line (BOMAC). The BOMAC phagocytic activity, reactive oxygen species production, and immune-related gene (IL6, IL10, IL12p40, IL13, IL23), transforming growth factor β, ARG1, CASP1, and inducible nitric oxide synthase expression were investigated when BOMAC were cocultured with cell wall components from 4 different strains (A, B, C, and D) and 2 forms of dead yeast from strain A. The BOMAC phagocytosis of mCherry-labeled MAP was concentration-dependently attenuated when BOMAC were cocultured with yeast components for 6 h. Each yeast derivative also induced a concentration-dependent increase in BOMAC reactive oxygen species production after a 6-h exposure. In addition, BOMAC mRNA expression of the immune-related genes was investigated after 6 and 24 h of exposure to yeast components. All yeast components were found to regulate the immunomodulatory genes of BOMAC; however, the response varied among components and over time. The in vitro bioassessment studies reported here suggest that dead yeast and its cell wall components may be useful for modulating macrophage function before or during MAP infection.

Abstract P4-06-12: Different patterns of risk reducing decisions in affected or unaffected BRCA mutation carriers

BACKGROUND

Risk-reducing (RR) management decreases the risk of breast cancer and BRCA related gynecologic cancer. However, there are fewer reports on the RR management in Asia compared to Western countries.The aim of this study is to identify risk reducing management patterns with BRCA1 or BRCA2 mutation carriers.

METHODS

The study group consisted of all consecutive 1104 breast cancer, ovarian patients and their families of high-risk patients who underwent BRCA gene testing in National Cancer Center, Korea from 2008 to 2016. A total 220 BRCA mutations (19.9%) were detected with 125(11.3%) of BRCA1 gene and 95 (8.6%) of BRCA2 gene.

RESULTS

Out of 220 BRCA mutations carriers, they were consisted of 83 breast cancers, 10 ovarian cancers, 7 both cancers, and 120 unaffected carriers. Among them, 42 were men and 178 were women. About 90 % (198/ 220) had the familial history of breast, ovarian or both malignancies (113 in BRCA1 and 85 in BRCA2 mutation (p=0.821)).

All 42 men chose surveillance. Among 178 female BRCA mutation carriers, 98(55.1%) underwent risk reducing management including 18(10.1%) of chemoprevention, and 80(49.9%) had risk-reducing surgeries (RRSs) (1 case of risk-reducing mastectomy, 76 of risk reducing bilateral salphingo-oophorectomy (RRSO), and 3 of both) and 80 (54.9%) chose only intensive surveillance for both of breast and ovary cancer.

In affected carriers with breast cancer, 59 (71.1%) underwent RR management (1 case of risk reducing mastectomy, 53 of RRSO, 3 of both surgery, and 2 of chemoprevention). There was no risk reducing management in affected carrier with ovarian cancer patients. In 78 unaffected women carriers, 39(50.0%) women received RR management (23(29.5%) cases of RRSO and 16(20.5%) cases of chemoprevention). The rates of RRSs have increased annually since the 2013 year, (prior to 2013 vs. since 2013, RRSs 28.6% (6 cases/21 carriers) vs. 37.2% (74/199), p&lt;0.01).

CONCLUSION

This study was conducted on the largest numbers of BRCA mutation carriers in Asian countries. RRSO is the more preferred management for affected carriers with breast cancer or unaffected carriers. The results might be explained by the severity of the illness and that RRSO was only reimbursed RR strategy from the Korean Government Insurance. Tailored genetic counseling and insurance policy may enhance overall levels of RR management.

Citation Format: Lee EG, Kang H, Park SJ, Han JH, Jung S-Y, Lee S, Kang H-S, Park B, Kong S-Y, Lim MC, Park S-Y, Lee ES. Different patterns of risk reducing decisions in affected or unaffected BRCA mutation carriers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-06-12.

Measurement of the Q^{2} Dependence of the Deuteron Spin Structure Function g_{1} and its Moments at Low Q^{2} with CLAS

We measured the g_{1} spin structure function of the deuteron at low Q^{2}, where QCD can be approximated with chiral perturbation theory (χPT). The data cover the resonance region, up to an invariant mass of W≈1.9  GeV. The generalized Gerasimov-Drell-Hearn sum, the moment Γ_{1}^{d} and the spin polarizability γ_{0}^{d} are precisely determined down to a minimum Q^{2} of 0.02  GeV^{2} for the first time, about 2.5 times lower than that of previous data. We compare them to several χPT calculations and models. These results are the first in a program of benchmark measurements of polarization observables in the χPT domain.