Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer

Mosaicism, the presence of subpopulations of cells bearing somatic mutations, is associated with disease and aging and has been detected in diverse tissues, including apparently normal cells adjacent to tumors. To analyze mosaicism on a large scale, we surveyed haplotype-specific somatic copy number alterations (sCNAs) in 1,708 normal-appearing adjacent-to-tumor (NAT) tissue samples from 27 cancer sites and in 7,149 blood samples from The Cancer Genome Atlas. We find substantial variation across tissues in the rate, burden and types of sCNAs, including those spanning entire chromosome arms. We document matching sCNAs in the NAT tissue and the adjacent tumor, suggesting a shared clonal origin, as well as instances in which both NAT tissue and tumor tissue harbor a gain of the same oncogene arising in parallel from distinct parental haplotypes. These results shed light on pan-tissue mutations characteristic of field cancerization, the presence of oncogenic processes adjacent to cancer cells.

The Nab experiment: A precision measurement of unpolarized neutron beta decay

Neutron beta decay is one of the most fundamental processes in nuclear physics and provides sensitive means to uncover the details of the weak interaction. Neutron beta decay can evaluate the ratio of axial-vector to vector coupling constants in the standard model, λ = gA/gV, through multiple decay correlations. The Nab experiment will carry out measurements of the electron-neutrino correlation parameter a with a precision of δa/a = 10−3 and the Fierz interference term b to δb = 3 × 10−3 in unpolarized free neutron beta decay. These results, along with a more precise measurement of the neutron lifetime, aim to deliver an independent determination of the ratio λ with a precision of δλ/λ = 0.03% that will allow an evaluation of Vud and sensitively test CKM unitarity, independent of nuclear models. Nab utilizes a novel, long asymmetric spectrometer that guides the decay electron and proton to two large area silicon detectors in order to precisely determine the electron energy and an estimation of the proton momentum from the proton time of flight. The Nab spectrometer is being commissioned at the Fundamental Neutron Physics Beamline at the Spallation Neutron Source at Oak Ridge National Lab. We present an overview of the Nab experiment and recent updates on the spectrometer, analysis, and systematic effects.

Early Maladaptive Schemas, Depression Severity, and Risk Factors for Persistent Depressive Disorder: a Cross-sectional Study

OBJECTIVE

To investigate associations of the five early maladaptive schemas (EMS) domains with depression severity by comparing patients with persistent depressive disorder (PDD), patients with major depressive disorder (MDD), and controls with no psychiatric disorders.

METHODS

Patients with PDD (n = 30), patients with MDD (n = 24), and controls with no psychiatric disorders (n = 30) were recruited. Participants were assessed using the Mini-International Neuropsychiatric Interview 5.0 version (MINI), the Beck Depression Inventory-Second Edition (BDI-II), and the Young Schema Questionnaire-3rd Edition Short Form (YSQ-S3).

RESULTS

The five EMS domains (YSQ-S3 score) significantly correlated with depression severity (BDI-II score), with correlation coefficients ranging from 0.583 to 0.788. After controlling for age, education, and sex, the two best predictors of depression severity were domains 'over-vigilance and inhibition' and 'disconnection and rejection'. For domains of disconnection and rejection, impaired autonomy and performance, and over-vigilance and inhibition, the total YSQ-S3 score was significantly higher in the PDD group than both the MDD and control groups. For the domain of impaired limits, the total YSQ-S3 score was significantly higher in both the PDD and MDD groups than the control group.

CONCLUSION

All five EMS domains correlated significantly with depression severity. PDD and MDD differed in psychopathology. The EMS domains of disconnection and rejection, impaired autonomy and performance, and over-vigilance and inhibition may be specific risk factors for PDD.

Volumetric laser endomicroscopy and its application to Barrett's esophagus: results from a 1,000 patient registry

Volumetric laser endomicroscopy (VLE) uses optical coherence tomography (OCT) for real-time, microscopic cross-sectional imaging. A US-based multi-center registry was constructed to prospectively collect data on patients undergoing upper endoscopy during which a VLE scan was performed. The objective of this registry was to determine usage patterns of VLE in clinical practice and to estimate quantitative and qualitative performance metrics as they are applied to Barrett's esophagus (BE) management. All procedures utilized the NvisionVLE Imaging System (NinePoint Medical, Bedford, MA) which was used by investigators to identify the tissue types present, along with focal areas of concern. Following the VLE procedure, investigators were asked to answer six key questions regarding how VLE impacted each case. Statistical analyses including neoplasia diagnostic yield improvement using VLE was performed. One thousand patients were enrolled across 18 US trial sites from August 2014 through April 2016. In patients with previously diagnosed or suspected BE (894/1000), investigators used VLE and identified areas of concern not seen on white light endoscopy (WLE) in 59% of the procedures. VLE imaging also guided tissue acquisition and treatment in 71% and 54% of procedures, respectively. VLE as an adjunct modality improved the neoplasia diagnostic yield by 55% beyond the standard of care practice. In patients with no prior history of therapy, and without visual findings from other technologies, VLE-guided tissue acquisition increased neoplasia detection over random biopsies by 700%. Registry investigators reported that VLE improved the BE management process when used as an adjunct tissue acquisition and treatment guidance tool. The ability of VLE to image large segments of the esophagus with microscopic cross-sectional detail may provide additional benefits including higher yield biopsies and more efficient tissue acquisition. Clinicaltrials.gov NCT02215291.

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2

Background

Gene expression-based profiling of colorectal cancer (CRC) can be used to identify four molecularly homogeneous consensus molecular subtype (CMS) groups with unique biologic features. However, its applicability to colorectal premalignant lesions remains unknown.

Patients and methods

We assembled the largest transcriptomic premalignancy dataset by integrating different public and proprietary cohorts of adenomatous and serrated polyps from sporadic (N = 311) and hereditary (N = 78) patient populations and carried out a comprehensive analysis of carcinogenesis pathways using the CMS random forest (RF) classifier.

Results

Overall, transcriptomic subtyping of sporadic and hereditary polyps revealed CMS2 and CMS1 subgroups as the predominant molecular subtypes in premalignancy. Pathway enrichment analysis showed that adenomatous polyps from sporadic or hereditary cases (including Lynch syndrome) displayed a CMS2-like phenotype with WNT and MYC activation, whereas hyperplastic and serrated polyps with CMS1-like phenotype harbored prominent immune activation. Rare adenomas with CMS4-like phenotype showed significant enrichment for stromal signatures along with transforming growth factor-β activation. There was a strong association of CMS1-like polyps with serrated pathology, right-sided anatomic location and BRAF mutations.

Conclusions

Based on our observations made in premalignancy, we propose a model of pathway activation associated with CMS classification in colorectal carcinogenesis. Specifically, while adenomatous polyps are largely CMS2, most hyperplastic and serrated polyps are CMS1 and may transition into other CMS groups during evolution into carcinomas. Our findings shed light on the transcriptional landscape of premalignant colonic polyps and may help guide the development of future biomarkers or preventive treatments for CRC.

High-Resolution Quantum Sensing with Shaped Control Pulses

We investigate the application of amplitude-shaped control pulses for enhancing the time and frequency resolution of multipulse quantum sensing sequences. Using the electronic spin of a single nitrogen-vacancy center in diamond and up to 10 000 coherent microwave pulses with a cosine square envelope, we demonstrate 0.6-ps timing resolution for the interpulse delay. This represents a refinement by over 3 orders of magnitude compared to the 2-ns hardware sampling. We apply the method for the detection of external ac magnetic fields and nuclear magnetic resonance signals of ^{13}C spins with high spectral resolution. Our method is simple to implement and especially useful for quantum applications that require fast phase gates, many control pulses, and high fidelity.

[Liposuction combined with lymphatico-venous anastomosis for treatment of secondary lymphedema of the lower limbs: a report of 49 cases]

Objective: To study the clinical effects of liposuction combined with lymphatico-venous anastomosis for treatment of secondary lymphedema of the lower limbs. Methods: A retrospective analysis was performed for 49 patients who had undergone liposuction combined with lymphatico-venous anastomosis to treat secondary lymphedema of the lower limbs at Department of Lymph Surgery, Beijing Shijitan Hospital from November 2013 to February 2015.All patients were female aging from 31 to 70 years with median age of (52±10)years.All patients had history of pelvic surgery.There were 32 cases with cervical carcinoma, 11 cases with endometrial cancer, 1 case with ovarian cancer who accepted radical hysterectomy, 2 cases with benign tumor who accepted resection, 2 cases accepted inguinal lymph node dissection, 1 case with rectal cancer accepted radical resection.There were 30 cases with history of radiation therapy and 23 cases with history of erysipelas recurrent((2.1±3.9)/year). The limb swelling degree in preoperative and postoperative patients was explored using one-way analysis of variance with replicate measures and paired sample t-test. Meanwhile the incidence of lymphogenous infection was used as an evaluation of operation efficacy. Results: The mean lower limb circumference difference at 7 days, 6 months and 12 months was (0.17±1.36)cm, (1.25±1.62)cm and(1.58±1.56)cm, respectively, which was significantly decreased compared with preoperative((4.92±2.16)cm) (t=-5.712, -5.777, -5.765; all P<0.01). The mean lower limb volume difference at 7 days, 6 months and 12 months was (522±799)ml, (726±973)ml and (889±895)ml, respectively, which was significantly decreased compared with preoperative((2 729±1 335) ml)(t=-5.905, -6.093, -5.777; all P<0.01). The incidence of erysipelas was 0.0(0.0, 0.0)/6 months within 6 months after operation and 0.0(0.0, 0.0)/6 months within 6-12 months after operation, which was significantly lower than that before operation(0.0(0.0, 2.0)/year). The feeling of tightness and heaviness of the limb was significantly improved compared with preoperative. Conclusion: Liposuction combined with lymphatico-venous anastomosis is an effective method for the treatment of secondary lymphedema of the lower limbs.

Active control of bright electron beams with RF optics for femtosecond microscopy

A frontier challenge in implementing femtosecond electron microscopy is to gain precise optical control of intense beams to mitigate collective space charge effects for significantly improving the throughput. Here, we explore the flexible uses of an RF cavity as a longitudinal lens in a high-intensity beam column for condensing the electron beams both temporally and spectrally, relevant to the design of ultrafast electron microscopy. Through the introduction of a novel atomic grating approach for characterization of electron bunch phase space and control optics, we elucidate the principles for predicting and controlling the phase space dynamics to reach optimal compressions at various electron densities and generating conditions. We provide strategies to identify high-brightness modes, achieving ∼100 fs and ∼1 eV resolutions with 10⁶ electrons per bunch, and establish the scaling of performance for different bunch charges. These results benchmark the sensitivity and resolution from the fundamental beam brightness perspective and also validate the adaptive optics concept to enable delicate control of the density-dependent phase space structures to optimize the performance, including delivering ultrashort, monochromatic, high-dose, or coherent electron bunches.

Nanoscale Imaging of Current Density with a Single-Spin Magnetometer

Charge transport in nanostructures and thin films is fundamental to many phenomena and processes in science and technology, ranging from quantum effects and electronic correlations in mesoscopic physics, to integrated charge- or spin-based electronic circuits, to photoactive layers in energy research. Direct visualization of the charge flow in such structures is challenging due to their nanometer size and the itinerant nature of currents. In this work, we demonstrate noninvasive magnetic imaging of current density in two-dimensional conductor networks including metallic nanowires and carbon nanotubes. Our sensor is the electronic spin of a diamond nitrogen-vacancy center attached to a scanning tip and operated under ambient conditions. Using a differential measurement technique, we detect DC currents down to a few μA with a current density noise floor of ∼2 × 10⁴ A/cm². Reconstructed images have a spatial resolution of typically 50 nm, with a best-effort value of 22 nm. Current density imaging offers a new route for studying electronic transport and conductance variations in two-dimensional materials and devices, with many exciting applications in condensed matter physics and materials science.

Development and Testing of in situ Materials for Human Exploration of Mars

Interplanetary space radiation poses a serious health hazard in long-term manned space missions. Natural Martian surface materials are evaluated for their potential use as radiation shields for manned Mars missions. The modified radiation fluences behind various kinds of Martian rocks and regolith are determined by solving the Boltzmann equation using NASA Langley’s HZETRN code along with the 1977 Solar Minimum galactic cosmic ray environmental model. To make structural shielding composite materials from constituents of the Martian atmosphere and from Martian regolith for Martian surface habitats, schemes for synthesizing polyimide from the Martian atmosphere and for processing Martian regolith/polyimide composites are proposed. Theoretical predictions of the shielding properties of these composites are computed to assess their shielding effectiveness. Adding high-performance polymer binders to Martian regolith to enhance the structural properties also enhances the shielding properties of these composites because of the added hydrogenous constituents. Laboratory testing of regolith simulant/polyimide composites is planned in order to validate this prediction and also to measure various structural properties.

Local dynamics of topological magnetic defects in the itinerant helimagnet FeGe

Chiral magnetic interactions induce complex spin textures including helical and conical spin spirals, as well as particle-like objects such as magnetic skyrmions and merons. These spin textures are the basis for innovative device paradigms and give rise to exotic topological phenomena, thus being of interest for both applied and fundamental sciences. Present key questions address the dynamics of the spin system and emergent topological defects. Here we analyse the micromagnetic dynamics in the helimagnetic phase of FeGe. By combining magnetic force microscopy, single-spin magnetometry and Landau–Lifschitz–Gilbert simulations we show that the nanoscale dynamics are governed by the depinning and subsequent motion of magnetic edge dislocations. The motion of these topologically stable objects triggers perturbations that can propagate over mesoscopic length scales. The observation of stochastic instabilities in the micromagnetic structure provides insight to the spatio-temporal dynamics of itinerant helimagnets and topological defects, and discloses open challenges regarding their technological usage.

Topological defects may strongly influence the evolution of a materials' micromagnetic structure whilst their manipulation forms the basis for emerging technological concepts. Here, the authors study the depinning and motion of magnetic edge dislocations in the domain structure of helimagnetic FeGe.