Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?

Field cancerization effects as well as isolated tumor cell foci extending well beyond the invasive tumor margin have been described previously to account for local recurrence rates following breast conserving surgery despite adequate surgical margins and breast radiotherapy. To look for evidence of possible tumor cell contamination or field cancerization by genetic effects, a pilot study (Study 1: 12 sample pairs) followed by a verification study (Study 2: 20 sample pairs) were performed on DNA extracted from HER2-positive breast tumors and matching normal adjacent mammary tissue samples excised 1-3 cm beyond the invasive tumor margin. High-resolution molecular inversion probe (MIP) arrays were used to compare genomic copy number variations, including increased HER2 gene copies, between the paired samples; as well, a detailed histologic and immunohistochemical (IHC) re-evaluation of all Study 2 samples was performed blinded to the genomic results to characterize the adjacent normal tissue composition bracketing the DNA-extracted samples. Overall, 14/32 (44 %) sample pairs from both studies produced genome-wide evidence of genetic aberrations including HER2 copy number gains within the adjacent normal tissue samples. The observed single-parental origin of monoallelic HER2 amplicon haplotypes shared by informative tumor-normal pairs, as well as commonly gained loci elsewhere on 17q, suggested the presence of contaminating tumor cells in the genomically aberrant normal samples. Histologic and IHC analyses identified occult 25-200 μm tumor cell clusters overexpressing HER2 scattered in more than half, but not all, of the genomically aberrant normal samples re-evaluated, but in none of the genomically normal samples. These genomic and microscopic findings support the conclusion that tumor cell contamination rather than genetic field cancerization represents the likeliest cause of local clinical recurrence rates following breast conserving surgery, and mandate caution in assuming the genomic normalcy of histologically benign appearing peritumor breast tissue

Reactivity of Zinc Finger Cysteines: Chemical Modifications Within Labile Zinc Fingers in Estrogen Receptor

Estrogen receptor (ER, alpha isoform) is a 67 kDa zinc finger transcription factor that plays a fundamental role in both normal reproductive gland development and breast carcinogenesis, and also represents a critical molecular target for breast cancer therapy. We are investigating the structural consequences of chemical exposures thought to modify essential zinc finger cysteine residues in human ER. The current study employs mass spectrometry to probe ER zinc finger structural changes induced by a redox-reactive vitamin K3 analog, menadione; a commonly used cysteine alkylator, iodoacetic acid; and a thiol alkylating fluorophore, monobromobimane. Although they are slower to react, the sterically bulkier reagents, monobromobimane and menadione, effectively alkylate the most susceptible ER zinc finger cysteine sulfhydryl groups. Menadione arylation results first in Michael addition of the hydroquinone followed by rapid oxidation to the corresponding quinone, evidenced by a 2 Da mass loss per cysteine residue. Mass spectrometric analysis performed under MALDI conditions reveals both hydroquinone and quinone forms of arylated menadione, whereas only the quinone product is detectable under ESI conditions. Tandem mass spectrometry of a synthetic peptide encompassing the C-terminal half of the structurally more labile second zinc finger of ER (ZnF2B) demonstrates that the two nucleophilic thiols in ZnF2B (Cys-237, Cys-240) are not chemically equivalent in their reactivity to bromobimane or menadione, consistent with their unequal positioning near basic amino acids that affect thiol pKa, thereby rendering Cys-240 more reactive than Cys-237. These findings demonstrate important differential susceptibility of ER zinc finger cysteine residues to thiol reactions

Assessing Soil and Potential Air Temperature Coupling Using PALM-4U: Implications for Idealized Scenarios

Underground heat extremes amplified by e.g., underground infrastructure or badly adjusted geothermal systems have long been discussed in geosciences. However, there is little emphasis on the exchange between these subsurface heat extremes and the atmosphere. To address the issue, this study investigates the impact of varying soil temperatures on potential air temperatures in an idealized domain using the turbulence and building resolving large eddy simulation urban micro-climate model PALM-4U. This involves two steps: first we test if and how idealized domains can be simulated, second the coupling between surface and subsurface energy fluxes or rather temperatures in air and soil are in focus. We develop several scenarios, distinguishing between cyclic or Dirichlet/radiation boundary conditions along the x-axis, between summer and winter, as well as between various land cover types. Our results demonstrate that cyclic boundary conditions induce modifications of the potential air temperatures due to changes in the soil temperature. The magnitude of the impact varies with respect to the tested land covers, which primarily affect absolute temperatures. Daytime and season have a larger influence on the magnitude of the modifications. A 5 K increase in subsurface temperatures at 2 m depth results in a maximum of a 0.38 K increase for near surface potential air temperatures in winter between 09:00 and 10:00 local time after three days of simulation. When soil temperatures are decreased, we find predominantly inverse patterns. The least influence is found during summer at 09:00 local time where the elevated soil temperatures increase potential air temperatures by only 0.02 K over short- and tall grass, and 0.18 K over bare soil. When using Dirichlet/radiation boundary conditions, the atmosphere cannot develop freely and changing soil temperatures do not impact potential air temperatures. These results help to enhance our understanding of the coupling between soil- and atmospheric temperatures and also provide recommendations for the simulability of idealized but reality-oriented scenarios in PALM-4U. It is one of the first studies that demonstrates that heat and cold sources in the soil can affect atmospheric parameters

Mass transfer in eccentric binaries: the new Oil-on-Water SPH technique

To measure the onset of mass transfer in eccentric binaries we have developed a two-phase SPH technique. Mass transfer is important in the evolution of close binaries, and a key issue is to determine the separation at which mass transfer begins. The circular case is well understood and can be treated through the use of the Roche formalism. To treat the eccentric case we use a newly-developed two phase system. The body of the donor star is made up from high-mass "water" particles, whilst the atmosphere is modelled with low-mass "oil" particles. Both sets of particles take part fully in SPH interactions. To test the technique we model circular mass-transfer binaries containing a 0.6 Msun donor star and a 1 Msun white dwarf; such binaries are thought to form cataclysmic variable (CV) systems. We find that we can reproduce a reasonable CV mass-transfer rate, and that our extended atmosphere gives a separation that is too large by aproximately 16%, although its pressure scale height is considerably exaggerated. We use the technique to measure the semi-major axis required for the onset of mass transfer in binaries with a mass ratio of q=0.6 and a range of eccentricities. Comparing to the value obtained by considering the instantaneous Roche lobe at pericentre we find that the radius of the star required for mass transfer to begin decreases systematically with increasing eccentricity.Comment: 9 pages, 8 figures, accepted by MNRA

Internal Crack Initiation and Growth Starting from Artificially Generated Defects in Additively Manufactured Ti6Al4V Specimen in the VHCF Regime

The aim of the present work was to investigate the ‘fine granular area’ (FGA) formation based on artificially generated internal defects in additively manufactured Ti6Al4V specimens in the early stage of fatigue crack growth in the ‘very high cycle fatigue’ (VHCF) regime. Fatigue tests were performed with constant amplitude at pure tension-compression loading (R = −1) using an ultrasonic fatigue testing setup. Failed specimens were investigated using optical microscopy, high-resolution ‘scanning electron microscopy’ (SEM), and ‘focused ion beam’ (FIB) techniques. Further, the paper introduces alternative proposals to identify the FGA layer beneath the fracture surfaces in terms of the ‘cross section polishing’ (CSP) technique and metallic grindings with special attention paid to the crack origin, the surrounding microstructure, and the expansion of the nanograin layer beneath the fracture surface. Different existing fracture mechanical approaches were applied to evaluate if an FGA formation is possible. Moreover, the results were discussed in comparison to the experimental findings

The dialectical experience of the fear of missing out for U.S. American iGen emerging adult college students

FoMO, the fear of missing out, is a salient and significant experience with personal and relational consequences. This study qualitatively analyzed 35 interviews with iGen emerging adult college students about their experiences with FoMO. Framed by relational dialectics theory 2.0 (Baxter, L. A. (2011). Voicing relationships: A dialogic perspective. Sage), we found two relational-level contradictions, connection and disconnection and inclusion and exclusion, which are illuminated by the cultural-level interplay of the discourses of ‘carpe diem’ and ‘investment in the future.’ Findings indicate that through the discourse of carpe diem, participants attempt to increase the power awarded to relational and personal resources and expand what it means to invest in the future. Implications of these findings related to well-being and academic success are discussed and practical applications for institutions of higher education such as team-based learning and more holistic professional development programs are presented

A Case Study of Small Scale Structure Formation in 3D Supernova Simulations

It is suggested in observations of supernova remnants that a number of large- and small-scale structures form at various points in the explosion. Multidimensional modeling of core-collapse supernovae has been undertaken since SN1987A, and both simulations and observations suggest/show that Rayleigh-Taylor instabilities during the explosion is a main driver for the formation of structure in the remnants. We present a case study of structure formation in 3D in a \msol{15} supernova for different parameters. We investigate the effect of moderate asymmetries and different resolutions of the formation and morphology of the RT unstable region, and take first steps at determining typical physical quantities (size, composition) of arising clumps. We find that in this progenitor the major RT unstable region develops at the He/OC interface for all cases considered. The RT instabilities result in clumps that are overdense by 1-2 orders of magnitude with respect to the ambient gas, have size scales on the level of a few % of the remnant diameter, and are not diffused after the first $\sim30$ yrs of the remnant evolution, in the absence of a surrounding medium.Comment: 59 pages, 34 figure

Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies

BACKGROUND: Recent studies indicate that microRNAs (miRNAs) are mechanistically involved in the development of various human malignancies, suggesting that they represent a promising new class of cancer biomarkers. However, previously reported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samples such as excision or core needle biopsies of breast or prostate cancer. Here we describe a novel combination of linear amplification and labeling of miRNA for highly sensitive expression microarray profiling requiring only picogram quantities of purified microRNA. RESULTS: Comparison of microarray and qRT-PCR measured miRNA levels from two different prostate cancer cell lines showed concordance between the two platforms (Pearson correlation R(2 )= 0.81); and extension of the amplification, labeling and microarray platform was successfully demonstrated using clinical core and excision biopsy samples from breast and prostate cancer patients. Unsupervised clustering analysis of the prostate biopsy microarrays separated advanced and metastatic prostate cancers from pooled normal prostatic samples and from a non-malignant precursor lesion. Unsupervised clustering of the breast cancer microarrays significantly distinguished ErbB2-positive/ER-negative, ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancer phenotypes (Fisher exact test, p = 0.03); as well, supervised analysis of these microarray profiles identified distinct miRNA subsets distinguishing ErbB2-positive from ErbB2-negative and ER-positive from ER-negative breast cancers, independent of other clinically important parameters (patient age; tumor size, node status and proliferation index). CONCLUSION: In sum, these findings demonstrate that optimized high-throughput microRNA expression profiling offers novel biomarker identification from typically small clinical samples such as breast and prostate cancer biopsies