[Value of prediction models for prognosis prediction of colorectal cancer: an analysis based on TCPA database]

OBJECTIVE

To assess the value of the combination of multiple proteins in predicting the prognosis of colorectal cancer (CRC) through bioinformatics analysis.

OBJECTIVE

The protein expression and clinical data were downloaded from TCPA database. Perl and R were used to screen the prognostic-related proteins, and through Cox analysis, the proteins that served as independent prognostic factors of CRC were identified to build the prediction model. Survival analyses were conducted for each of the proteins included in the prediction model and the risk score of the model, and risk curves was drawn for the risk score and the patients' survival status to verify the performance of the model. Independent prognosis analysis and ROC analysis were used to assess the value and advantages of the model in prognosis prediction. The interactions between the proteins included in the model and the differential expressions of the key genes related with the proteins were analyzed.

OBJECTIVE

Six proteins were screened for model construction. Compared with a single gene, the model showed much greater prognostic value for CRC. Independent prognostic analysis showed that the risk score of the prediction model was significantly related with the prognosis (P < 0.001), and the model could be used as an independent risk factor for prognostic assessment of the patients. ROC analysis showed that the model had good specificity and sensitivity for prognostic prediction (AUC=0.734). Protein interactions showed that BID, SLC1A5 and SRC_pY527 were significantly correlated with other proteins (P < 0.001), and SLC1A5 and SRC_pY527 had the most significant interactions with other proteins (P < 0.001). Except for those of INPP4B, the key genes related with the proteins in the prediction model had significant differential expressions at the mRNA level in CRC (P < 0.05).

OBJECTIVE

The prediction model constructed based on 6 proteins has good prognostic value for CRC. The proteins SLC1A5 and SRC_pY527 play key roles in the prognosis of CRC, and SRC_pY527 may regulate the occurrence and progression of CRC through the SRC/AKT/MAPK signal axis and thus may serve as a new therapeutic target of CRC.

[Metabolism and transport pathway of prostaglandin E2 and its role in liver regeneration]

The liver is an organ with regenerative capacity and is essential for maintaining the body homeostasis. Under pathological conditions, such as chronic hepatitis, liver cirrhosis and so on, the impairment of liver regeneration can lead to insufficient liver function or even liver failure. Therefore, promoting liver regeneration can improve the patient's prognosis. Prostaglandin E2 is a hormone-like messenger with physiological activity that can promote tissue regeneration. This article reviews the metabolism and transport pathways of prostaglandin E2 and its mechanism of action in liver tissue regeneration, and proposes that prostaglandin E2 is an important cytokine involved in the liver regeneration process, and has potential clinical application prospects for the treatment of liver injury.

Local negative permittivity and topological phase transition in polar skyrmions

Topological solitons such as magnetic skyrmions have drawn attention as stable quasi-particle-like objects. The recent discovery of polar vortices and skyrmions in ferroelectric oxide superlattices has opened up new vistas to explore topology, emergent phenomena and approaches for manipulating such features with electric fields. Using macroscopic dielectric measurements, coupled with direct scanning convergent beam electron diffraction imaging on the atomic scale, theoretical phase-field simulations and second-principles calculations, we demonstrate that polar skyrmions in (PbTiO₃)_n/(SrTiO₃)_n superlattices are distinguished by a sheath of negative permittivity at the periphery of each skyrmion. This enhances the effective dielectric permittivity compared with the individual SrTiO₃ and PbTiO₃ layers. Moreover, the response of these topologically protected structures to electric field and temperature shows a reversible phase transition from the skyrmion state to a trivial uniform ferroelectric state, accompanied by large tunability of the dielectric permittivity. Pulsed switching measurements show a time-dependent evolution and recovery of the skyrmion state (and macroscopic dielectric response). The interrelationship between topological and dielectric properties presents an opportunity to simultaneously manipulate both by a single, and easily controlled, stimulus, the applied electric field.

[Simultaneous combined radical surgery for hepatic and renal alveolar echinococcosis: an analysis of 10 clinical cases]

Objective: To examine the feasibility, safety and efficacy of simultaneous combined radical surgery for hepatic and renal alveolar echinococcosis (AE). Methods: Clinical dates of consecutive 10 hepatic and renal AE patients who accepted surgical treatment in the First Affiliated Hospital of Xinjiang Medical University during April 2013 to September 2019 were analyzed retrospectively. There were 8 males and 2 females, aged (42.5±10.3) years (range: 27 to 52 years). Seven of them had previously palliative surgical treatment with poor compliance to post-operative medication. All of the patients had hepatic-renal combined AE lesions, and two of them had left lateral and left renal lesions for each, which sized for (726.4±576.1)cm³ (range: 117.0 to 1 998.0 cm³). Extra-hepatic or renal lesions infiltrated to right diaphragm, inferior vena cava, right adrenal gland, abdominal wall, right psoas muscle, duodenum wall and right pulmonary lobe (respectively were 7, 7, 6, 2, 1, 1, 2 cases). Surgery were performed mainly with simultaneous combined surgery and vascular reconstruction techniques for this series. Hemi-hepatectomy or extended right lobectomy was applied in 8 patients, while 2 other patients received ex vivo liver resection and autotransplantation, additionally, one patient had partial hepatectomy for left lateral lobular lesion. Total right nephrectomy, partial right nephrectomy and partial left nephrectomy were respectively performed on 7, 3 and 1 patient(s). Additionally, extra-hepatic or renal lesions were eradicated followed by relevant repairments or reconstructions. Results: Surgeries went well and there was no intra-or post-operative liver or renal dysfunction occurred. During recovery period, 3 cases experienced with hydrothorax and managed well after drainage and supportive treatment, and one patient developed peri-renal urinary leakage and cured by "J" catheter. The subjects were followed-up for 6 to 81 months (median: 21 months), no death, organ dysfunction, chronic or acute kidney diseases occurred. One case encountered with abdominal hernia at post-operative 7^th month and was successfully managed with laparoscopic repair with artificial mesh. No disease recurrence in all patients, which reached clinical cure at last. Conclusion: When complied strictly to indications, simultaneous combined radical surgery could be a feasible, safe and efficient approach for patients with hepatic and renal AE, which is primary or relapsed from previous hepatic AE surgery or interventional therapies as well as neighboring organ AE invasions.

Neutron sub-micrometre tomography from scattering data

Neutrons are valuable probes for various material samples across many areas of research. Neutron imaging typically has a spatial resolution of larger than 20 µm, whereas neutron scattering is sensitive to smaller features but does not provide a real-space image of the sample. A computed-tomography technique is demonstrated that uses neutron-scattering data to generate an image of a periodic sample with a spatial resolution of ∼300 nm. The achieved resolution is over an order of magnitude smaller than the resolution of other forms of neutron tomography. This method consists of measuring neutron diffraction using a double-crystal diffractometer as a function of sample rotation and then using a phase-retrieval algorithm followed by tomographic reconstruction to generate a map of the sample's scattering-length density. Topological features found in the reconstructions are confirmed with scanning electron micrographs. This technique should be applicable to any sample that generates clear neutron-diffraction patterns, including nanofabricated samples, biological membranes and magnetic materials, such as skyrmion lattices.

Cogeneration of hot electrons from multiple laser-plasma instabilities

Interactions of two-plasmon decay (TPD) and side-stimulated Raman scattering (SSRS) were studied using three-dimensional particle-in-cell simulations under inertial-confinement-fusion-relevant conditions for linearly and circularly polarized lasers. In the linear stage, SSRS took place under n_{e}=0.235n_{c} and TPD dominated near the quarter-critical density surface and their growth rates agreed with theory. In the nonlinear stage, SSRS reduced TPD through pump depletion. Hot electrons were found to be first accelerated by SSRS plasma waves and then by TPD plasma waves through a cogeneration mechanism. Compared to the linearly polarized case with the same laser intensity, both SSRS and TPD were reduced due to the lower laser amplitude in the circularly polarized case. As a result, a 30% decrease in hot electron flux was observed.

Clinical characteristics and radiological features of children infected with the 2019 novel coronavirus

AIM

To identify and summarise the common findings from 2019 novel coronavirus (2019-nCoV) infections in children.

MATERIALS AND METHODS

The clinical characteristics and radiological findings (chest radiography and chest computed tomography [CT]) of nine children infected with the 2019-nCoV were reviewed in this retrospective case series.

RESULTS

Among the children, six had fever (including two children with cough), one had only cough, one had a stuffy nose when initially diagnosed, and one was an asymptomatic carrier. Chest radiographs seemed mostly normal in six cases whereas increased and/or disordered bilateral bronchovascular shadows and dense hilar shadows were seen in three cases. Chest CT exhibited no obvious abnormal signs in four cases. Typical CT findings included patchy, peripheral ground-grass opacities, subpleural lamellar dense shadows, and parenchymal bands. Pleural effusions, mediastinal lymphadenopathy, cavitation, and pleural thickening were absent.

CONCLUSION

The clinical manifestations and radiological findings of the 2019-nCoV-infected children were mild and lacked a typical pattern.

Pump depletion and hot-electron generation in long-density-scale-length plasma with shock-ignition high-intensity laser

Two-dimensional particle-in-cell simulations for laser plasma interaction with laser intensity of 10^{16}W/cm^{2}, plasma density range of 0.01-0.28n_{c}, and scale length of 230-330μm showed significant pump depletion of the laser energy due to stimulated Raman scattering (SRS) and stimulated Brillouin scattering (SBS) in the low-density region (n_{e}=0.01-0.2n_{c}). The simulations identified hot electrons generated by SRS in the low-density region with moderate energy and by two-plasmon-decay near n_{e}=0.25n_{c} with higher energy. The overall hot electron temperature (46 keV) and conversion efficiency (3%) were consistent with the experiment's measurements. The simulations also showed artificially reducing SBS would lead to stronger SRS and a softer hot-electron spectrum.

Are left ventricular muscle area and radiation attenuation associated with overall survival in advanced pancreatic cancer patients treated with chemotherapy?

AIM

To evaluate whether cardiac muscle area and radiation attenuation, determined using pre-chemotherapy computed tomography (CT), are associated with therapeutic response and overall survival (OS) in chemotherapy-treated advanced pancreatic cancer (APC) patients.

MATERIALS AND METHODS

Ninety-eight chemotherapy-treated APC patients who underwent pre-chemotherapy CT between 2009 and 2018 were considered. Left ventricular muscle area (LVMA) and left ventricular muscle radiation attenuation (LVMRA) were measured using pre-chemotherapy arterial-phase CT. OS and progression-free survival (PFS) were analysed using Kaplan-Meier curves. Univariate and multivariate Cox regression analyses were performed to analyse potential factors affecting OS and PFS.

RESULTS

Patients with low LVMRA, low LVMA at baseline CT, and multiple metastases had a significantly shorter median OS than patients with high LVMRA, high LVMA, and without multiple metastases (8.8 versus 14 months, p=0.017; 12.2 versus 18.1 months, p=0.038; 7.3 versus 13.5 months, p<0.001, respectively). Patients with low LVMRA and distant metastasis had a shorter median PFS than patients with high LVMRA and those without distant metastasis (4.9 versus 8.3 months, p=0.032; 5.4 versus 9.9 months, p=0.002, respectively). Moreover, the mean LVMRA was the highest in the partial response group (p=0.028).

CONCLUSION

LVMRA could well predict PFS and OS in chemotherapy-treated APC patients.

Three-dimensional particle-in-cell modeling of parametric instabilities near the quarter-critical density in plasmas

The nonlinear regime of laser-plasma interactions including both two-plasmon decay (TPD) and stimulated Raman scattering (SRS) instabilities has been studied in three-dimensional (3D) particle-in-cell simulations with parameters relevant to the inertial confinement fusion (ICF) experiments. SRS and TPD develop in the same region in plasmas, and the generation of fast electrons can be described accurately with only the full model including both SRS and TPD. The growth of instabilities in the linear stage is found to be in good agreement with analytical theories. In the saturation stage the low-frequency density perturbations driven by the daughter waves of the SRS side scattering can saturate the TPD and consequently inhibit the fast-electron generation. The fast-electron flux in 3D modeling is up to an order of magnitude smaller than previously reported in 2D TPD simulations, bringing it close to the results of ICF experiments.

Self-Generated Magnetic and Electric Fields at a Mach-6 Shock Front in a Low Density Helium Gas by Dual-Angle Proton Radiography

Shocks are abundant both in astrophysical and laboratory systems. While the electric fields generated at shock fronts have recently attracted great attention, the associated self-generated magnetic field is rarely studied, despite its ability to significantly affect the shock profile in the nonideal geometry where density and temperature gradients are not parallel. We report here the observation of a magnetic field at the front of a Mach ∼6 shock propagating in a low-density helium gas system. Proton radiography from different projection angles not only confirms the magnetic field's existence, but also provides a quantitative measurement of the field strength in the range ∼5 to 7 T. X-ray spectrometry allowed inference of the density and temperature at the shock front, constraining the plasma conditions under which the magnetic and electric fields are generated. Simulations with the particle-in-cell code lsp attribute the self-generation of the magnetic field to the Biermann battery effect (∇n_{e}×∇T_{e}).

Optical creation of a supercrystal with three-dimensional nanoscale periodicity

Stimulation with ultrafast light pulses can realize and manipulate states of matter with emergent structural, electronic and magnetic phenomena. However, these non-equilibrium phases are often transient and the challenge is to stabilize them as persistent states. Here, we show that atomic-scale PbTiO₃/SrTiO₃ superlattices, counterpoising strain and polarization states in alternate layers, are converted by sub-picosecond optical pulses to a supercrystal phase. This phase persists indefinitely under ambient conditions, has not been created via equilibrium routes, and can be erased by heating. X-ray scattering and microscopy show this unusual phase consists of a coherent three-dimensional structure with polar, strain and charge-ordering periodicities of up to 30 nm. By adjusting only dielectric properties, the phase-field model describes this emergent phase as a photo-induced charge-stabilized supercrystal formed from a two-phase equilibrium state. Our results demonstrate opportunities for light-activated pathways to thermally inaccessible and emergent metastable states.

Three Phase-Grating Moiré Neutron Interferometer for Large Interferometer Area Applications

We demonstrate a three phase-grating moiré neutron interferometer in a highly intense neutron beam as a robust candidate for large area interferometry applications and for the characterization of materials. This novel far-field moiré technique allows for broad wavelength acceptance and relaxed requirements related to fabrication and alignment, thus circumventing the main obstacles associated with perfect crystal neutron interferometry. We observed interference fringes with an interferometer length of 4 m and examined the effects of an aluminum 6061 alloy sample on the coherence of the system. Experiments to measure the autocorrelation length of samples and the universal gravitational constant are proposed and discussed.

Abstract PD1-15: The landscape of somatic genetic alterations in breast cancers from ATM germline mutation carriers

Introduction:Pathogenic and/or founder germline variants in the ataxia-telangiectasia mutated (ATM) gene confer an increased breast cancer (BC) risk. The protein kinase ATM plays a central role inDNA double-strand break-repair and in the activation of downstream targets such as p53 and BRCA1. We sought to define the repertoire of somatic genetic alterations of BCs from patients with pathogenic germline ATM mutations and whether somatic loss of heterozygosity (LOH) of ATM would be present in these cancers.

Methods: 21 BCs from ATM germline mutation carriers were microdissected. Tumor and normal DNA samples were subjected to whole-exome sequencing (WES, n=12) or massively parallel sequencing targeting all coding regions and selected intronic and regulatory regions of 410 key cancer genes (n=9). Somatic mutations, copy number alterations, cancer cell fractions, large-scale state transitions (LSTs) and mutational signatures were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to assess LOH of the wild-type allele of ATM.

Results: Of the patients included in this study, 71%, 24% and 5% of cases harbored ATM missense (all but one p.V2424G), frame-shift and nonsense germline mutations, respectively. All tumors were ER-positive and four (19%) were HER2-positive. The median age of the patients was 46 years (32–79 years). Our analyses revealed biallelic inactivation of ATM through LOH of the wild-type allele in 16 of 21 cases (76%), and second somatic ATM mutations were not found. The median number of non-synonymous somatic mutations was 38 (range 15-113) and 2 (range 0-8)in tumors subjected to WES and targeted sequencing, respectively. The repertoire of somatic genetic alterations of ATM-associated BCs was found to be heterogeneous, including clonal PIK3CA mutations (24%), GATA3 mutations (19%), FANCI amplifications (19%) and CCND1 amplifications (14%). Importantly, however, no somatic mutations affecting TP53 were found. Analysis of the WES data revealed that 5 (42%) ATM-associated BCs displayed high LST scores, all of which harbored bi-allelic ATM inactivation. In contrast to BRCA1- and BRCA2-associated BCs, which frequently display the mutational signature 3 associated with defective homologous recombination DNA repair, the ATM-associated BCs studied displayed the ageing mutational signature (i.e. signature 1). Comparison of the mutational profiles of the ATM--associated BCs subjected to WES (n=12) with those of BRCA1- (n=11) and BRCA2-associated (n=10) BCs from The Cancer Genome Atlas revealed that TP53 was more frequently mutated in BCs from BRCA1 germline mutation carriers (0% vs 72%, P&lt;0.001), while no differences with BRCA2-associated BCs were found.

Conclusion: ATM-associated BCs frequently display bi-allelic ATM inactivation through LOH of the wild-type allele and a subset of these cases displayed high levels of LSTs. These findings suggest that at least in a subset of ATM-associated BCs, biallelic inactivation of ATM rather than a dominant negative effect of the germline mutation may be the mechanism of inactivation of this tumor suppressor gene. The repertoire of somatic genetic alterations of ATM-associated BCs is heterogeneous, with a noticeable lack of TP53 somatic mutations.

Citation Format: Weigelt B, Bi R, Kumar R, James PA, Thorne H, Couch FJ, Eccles DM, Blows F, Geyer FC, Li A, Selenica P, Lim RS, Blecua P, Shen R, Wen H, Robson ME, Reis-Filho JS, Chenevix-Trench G. The landscape of somatic genetic alterations in breast cancers from ATM germline 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 PD1-15.