Regional Strucutal Cross Sections, Mid-Permian to Quaternary Strata, Texas Panhandle and Eastern New Mexico

The Palo Duro and Dalhart Basins of the Texas Panhandle and eastern New Mexico contain bedded Permian salts of sufficient thickness and depth to be considered potential sites for long-term storage and isolation of high-level nuclear waste. Salt (primarily halite) is a desirable host rock because of its low permeability, high thermal conductivity, low moisture content, and high gamma-ray shielding properties (Johnson, 1976b). A major concern that must be addressed if nuclear waste is to be stored in the Texas Panhandle is the long-term integrity of the bedded-salt host rock. Areas where salt has been removed by dissolution have been identified beneath the Southern High Plains, along the eastern and western escarpments of the Southern High Plains, and along the Canadian River valley (Gustavson and others, 1980b; Presley, 1980a, 1980b). Region I cross sections of mid-Permian to Quaternary strata in the Texas Panhandle and eastern New Mexico illustrate lithologic and structural relations that are interpreted to have resulted from the regional dissolution of salt and the collapse of overlying strata. The cross sections were constructed using gamma-ray logs, sample logs, and surface geologic maps (Handford, 1980a; McGillis, 1980). Gamma-ray logs are shown on the cross sections because they best demonstrate variations in evaporite strata. Figure 1 is an index map depicting the locations of the cross sections. Stratigraphic nomenclature used on the cross sections is given in table 1.Bureau of Economic Geolog

Joint and individual analysis of breast cancer histologic images and genomic covariates

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics

Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types

Background: Immune infiltration of the tumor microenvironment has been associated with improved survival for some patients with solid tumors. The precise makeup and prognostic relevance of immune infiltrates across a broad spectrum of tumors remain unclear

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. In simulation, the integrated DNA and RNA model outperformed the DNA-WES only model. Validation by patient-matched whole genome sequencing demonstrated superior performance of the integrated model over DNA-WES only models, including a published method and published mutation profiles. Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. RNA provided greater mutation signal than DNA in expressed mutations. Compared to earlier studies on this cohort, UNCeqR increased mutation rates of driver and therapeutically targeted genes (e.g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors

Nuclear Localized LSR: A Novel Regulator of Breast Cancer Behavior and Tumorigenesis

Lipolysis Stimulated Lipoprotein Receptor (LSR) has been found in the plasma membrane and is believed to function in lipoprotein endocytosis and tight junctions. Given the impact of cellular metabolism and junction signaling pathways on tumor phenotypes and patient outcome, it is important to understand how LSR cellular localization mediates its functions. We conducted localization studies, evaluated DNA binding, and examined the effects of nuclear LSR in cells, xenografts, and clinical specimens. We found LSR within the membrane, cytoplasm, and the nucleus of breast cancer cells representing multiple intrinsic subtypes. Chromatin immunoprecipitation (ChIP) showed direct binding of LSR to DNA, and sequence analysis identified putative functional motifs and post-translational modifications of the LSR protein. While neither overexpression of transcript variants, nor pharmacological manipulation of post-translational modification significantly altered localization, inhibition of nuclear export enhanced nuclear localization, suggesting a mechanism for nuclear retention. Co-immunoprecipitation and proximal ligation assays indicated LSR-pericentrin interactions, presenting potential mechanisms for nuclear-localized LSR. The clinical significance of LSR was evaluated using data from over 1,100 primary breast tumors, which showed high LSR levels in basal-like tumors and tumors from African-Americans. In tumors histosections, nuclear localization was significantly associated with poor outcomes. Finally, in vivo xenograft studies revealed that basal-like breast cancer cells that over-express LSR exhibited both membrane and nuclear localization, and developed tumors with 100% penetrance, while control cells lacking LSR developed no tumors. These results show that nuclear LSR alters gene expression and may promote aggressive cancer phenotypes

Live Coding, Live Notation, Live Performance

This paper/demonstration explores relationships between code, notation including representation, visualisation and performance. Performative aspects of live coding activities are increasingly being investigated as the live coding movement continues to grow and develop. Although live instrumental performance is sometimes included as an accompaniment to live coding, it is often not a fully integrated part of the performance, relying on improvisation and/or basic indicative forms of notation with varying levels of sophistication and universality. Technologies are developing which enable the use of fully explicit music notations as well as more graphic ones, allowing more fully integrated systems of code in and as performance which can also include notations of arbitrary complexity. This itself allows the full skills of instrumental musicians to be utilised and synchronised in the process. This presentation/demonstration presents work and performances already undertaken with these technologies, including technologies for body sensing and data acquisition in the translation of the movements of dancers and musicians into synchronously performable notation, integrated by live and prepared coding. The author together with clarinetist Ian Mitchell present a short live performance utilising these techniques, discuss methods for the dissemination and interpretation of live generated notations and investigate how they take advantage of instrumental musicians’ training-related neuroplasticity skills

Inelastic Scattering Time for Conductance Fluctuations

We revisit the problem of inelastic times governing the temperature behavior of the weak localization correction and mesoscopic fluctuations in one- and two-dimensional systems. It is shown that, for dephasing by the electron electron interaction, not only are those times identical but the scaling functions are also the same.Comment: 10 pages Revtex; 5 eps files include

A Global Community of Courts? Modelling the Use of Persuasive Authority as a Complex Network

There is a growing discussion in the legal literature of an emerging global community of courts composed of a network of increasing judicial dialogue across national borders. We investigate the use of foreign persuasive authority in common law countries by analyzing the network of citations to case law in a corpus of over 1.5 million judgments given by the senior courts of twenty-six common law countries. Our corpus of judgments is derived from data available in the vLex Justis database. In this paper we aim to quantify the flow of jurisprudence across the countries in our corpus and to explore the factors that may influence a judge’s selection of foreign jurisprudence. Utilization of foreign case law varies across the countries in our data, with the courts of some countries presenting higher engagement with foreign jurisprudence than others. Our analysis shows that there has been an upward trend in the use of foreign case law over time, with a marked increase in citations across national borders from the 1990s onward, potentially indicating that increased digital access to foreign judgments has served to facilitate and promote comparative analysis. Not only has the use of foreign case law generally increased over time, the factors that may influence the selection of case law have also evolved, with judges gradually casting their research beyond the most influential and well-known foreign authorities. Notwithstanding that judgments emanating from the United Kingdom (chiefly from the courts of England and Wales) constitute the most frequently consulted body of jurisprudence, we find evidence that domestic courts favor citing the case law of countries that are geographically proximal

Intratumor Heterogeneity of the Estrogen Receptor and the Long-term Risk of Fatal Breast Cancer.

Background:Breast cancer patients with estrogen receptor (ER)-positive disease have a continuous long-term risk for fatal breast cancer, but the biological factors influencing this risk are unknown. We aimed to determine whether high intratumor heterogeneity of ER predicts an increased long-term risk (25 years) of fatal breast cancer. Methods:The STO-3 trial enrolled 1780 postmenopausal lymph node-negative breast cancer patients randomly assigned to receive adjuvant tamoxifen vs not. The fraction of cancer cells for each ER intensity level was scored by breast cancer pathologists, and intratumor heterogeneity of ER was calculated using Rao's quadratic entropy and categorized into high and low heterogeneity using a predefined cutoff at the second tertile (67%). Long-term breast cancer-specific survival analyses by intra-tumor heterogeneity of ER were performed using Kaplan-Meier and multivariable Cox proportional hazard modeling adjusting for patient and tumor characteristics. Results:A statistically significant difference in long-term survival by high vs low intratumor heterogeneity of ER was seen for all ER-positive patients (P < .001) and for patients with luminal A subtype tumors (P = .01). In multivariable analyses, patients with high intratumor heterogeneity of ER had a twofold increased long-term risk as compared with patients with low intratumor heterogeneity (ER-positive: hazard ratio [HR] = 1.98, 95% confidence interval [CI] = 1.31 to 3.00; luminal A subtype tumors: HR = 2.43, 95% CI = 1.18 to 4.99). Conclusions:Patients with high intratumor heterogeneity of ER had an increased long-term risk of fatal breast cancer. Interestingly, a similar long-term risk increase was seen in patients with luminal A subtype tumors. Our findings suggest that intratumor heterogeneity of ER is an independent long-term prognosticator with potential to change clinical management, especially for patients with luminal A tumors

What do we teach when we teach the Learning Sciences? A document analysis of 75 graduate programs

The learning sciences, as an academic community investigating human learning, emerged more than 30 years ago. Since then, graduate learning sciences programs have been established worldwide. Little is currently known, however, about their disciplinary backgrounds and the topics and research methods they address. In this document analysis of the websites of 75 international graduate learning sciences programs, we examine central concepts and research methods across institutions, compare the programs, and assess the homogeneity of different subgroups. Results reveal that the concepts addressed most frequently were real-world learning in formal and informal contexts, designing learning environments, cognition and metacognition, and using technology to support learning. Among research methods, design-based research (DBR), discourse and dialog analyses, and basic statistics stand out. Results show substantial differences between programs, yet programs focusing on DBR show the greatest similarity regarding the other concepts and methods they teach. Interpreting the similarity of the graduate programs using a community of practice perspective, there is a set of relatively coherent programs at the core of the learning sciences, pointing to the emergence of a discipline, and a variety of multidisciplinary and more heterogeneous programs “orbiting” the core in the periphery, shaping and innovating the field