Accounting for Environmental and Anthropogenic Factors: Approaches to enhancing horizontal resolution and interpretability in geophysical surveys

Common hindrances in geophysical survey, whether small-scale or landscape, are modern rubbish, rubble, ferrous objects, groundwater, and/or high attenuation materials. Groundwater and high attenuation materials greatly reduce the maximum potential depth of investigation. In an attempt to overcome these obstacles, surveys were conducted at the Dominican Friary in Trim, Ireland, which aimed to refine standard survey protocols for achieving high-resolution data from single channel ground-penetrating radar (GPR) surveys of small areas (<1ha). Based on the surveys’ results, it was determined that, for single channel GPR surveys utilising a central antenna frequency between 250MHz and 500MHz, a 0.1m traverse interval will maximise the potential to delineate targets smaller than 2.5m2, though for time efficient surveys, a traverse interval less than 25% the size of a discrete target (where the target is at least 1.5m2) provides adequate raw data to delineate significant anomalies. It is hoped that these parameters can also be applied to multichannel systems in due course. Subsequent trials of these survey parameters were conducted at the Tràng An Landscape Complex (Ninh Binh, Vietnam) as part of the SUNDASIA Project, where stratigraphic changes and discrete areas of anthropogenic activity in response to climate change were investigated. Applications of high resolution data acquisition methods proved successful within this environment, as GPR delineated discrete changes in high attenuation soil. Ultimately, these case studies demonstrate the success of small area surveys which face environmental challenges. Further analysis of the success rate of these parameters is to be expected at sites throughout southwest England and Ireland

Exploring Typology Categorizations of Male Perpetrators: A Methodology Study

Intimate partner violence (IPV) perpetrators were categorized based on whether they were generally violent (GV) or family only violent (FO) using self-report or arrest records. Classification criteria to assess recidivism in perpetrators of IPV were evaluated herein to determine the incremental validity of using a perpetrator’s criminal history in addition to their self-report information for categorization purposes. The concordance rates for categorizing subtypes of male perpetrators were compared for two methods, namely, self-report versus criminal history data. Categorizations were made based on self-reported history of violence and federal criminal records separately. Between measures consistency was defined as whether or not the self-report categorizations matched federal criminal record categorizations. It was hypothesized that self-report would not be sufficient as the sole method of categorizing male perpetrators, and the use of criminal history data would add to the validity of the categorization system. Self-reports of aggression were higher than criminal records of aggression. Using data sources together may yield the best outcomes for offenders and society. Implications are discussed

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : BAO measurement from the LOS-dependent power spectrum of DR12 BOSS galaxies

HGM is grateful for support from the UK Science and Technology Facilities Council through the grant ST/I001204/1. WJP is grateful for support from the UK Science and Technology Facilities Research Council through the grant ST/I001204/1, and the European Research Council through the grant “Darksurvey”, reference 614030. FSK acknowledges the support of the Karl-Schwarzschild Program from the Leibniz Society.[abridged] We present an anisotropic analysis of the baryonic acoustic oscillation (BAO) scale in the twelfth and final data release of the Baryonic Oscillation Spectroscopic Survey (BOSS). We independently analyse the LOWZ and CMASS galaxy samples: the LOWZ sample contains contains 361\,762 galaxies with an effective redshift of $z_{\rm LOWZ}=0.32$, and the CMASS sample consists of 777\,202 galaxies with an effective redshift of $z_{\rm CMASS}=0.57$. We extract the BAO peak position from the monopole power spectrum moment, $\alpha_0$, and from the $\mu^2$ moment, $\alpha_2$. We report $H(z_{\rm LOWZ})r_s(z_d)=(11.64\pm0.62)\cdot10^3\,{\rm km}s^{-1}$ and $D_A(z_{\rm LOWZ})/r_s(z_d)=6.85\pm0.17$ with a cross-correlation coefficient of $r_{HD_A}=0.42$, for the LOWZ sample; and $H(z_{\rm CMASS})r_s(z_d)=(14.56\pm0.38)\cdot10^3\,{\rm km}s^{-1}$ and $D_A(z_{\rm CMASS})/r_s(z_d)=9.42\pm0.13$ with a cross-correlation coefficient of $r_{HD_A}=0.51$, for the CMASS sample. We combine these results with the measurements of the BAO peak position in the monopole and quadrupole correlation function of the same dataset \citep[][companion paper]{Cuestaetal2015} and report the consensus values: $H(z_{\rm LOWZ})r_s(z_d)=(11.64\pm0.70)\cdot10^3\,{\rm km}s^{-1}$ and $D_A(z_{\rm LOWZ})/r_s(z_d)=6.76\pm0.15$ with $r_{HD_A}=0.35$ for the LOWZ sample; and $H(z_{\rm CMASS})r_s(z_d)=(14.66\pm0.42)\cdot10^3\,{\rm km}s^{-1}$ and $D_A(z_{\rm CMASS})/r_s(z_d)=9.47\pm0.13$ with $r_{HD_A}=0.54$ for the CMASS sample.Publisher PDFPeer reviewe

A novel prostate cancer subtyping classifier based on luminal and basal phenotypes

Background: Prostate cancer (PCa) is a clinically heterogeneous disease. The creation of an expression-based subtyping model based on prostate-specific biological processes was sought. Methods: Unsupervised machine learning of gene expression profiles from prospectively collected primary prostate tumors (training, n = 32,000; evaluation, n = 68,547) was used to create a prostate subtyping classifier (PSC) based on basal versus luminal cell expression patterns and other gene signatures relevant to PCa biology. Subtype molecular pathways and clinical characteristics were explored in five other clinical cohorts. Results: Clustering derived four subtypes: luminal differentiated (LD), luminal proliferating (LP), basal immune (BI), and basal neuroendocrine (BN). LP and LD tumors both had higher androgen receptor activity. LP tumors also had a higher expression of cell proliferation genes, MYC activity, and characteristics of homologous recombination deficiency. BI tumors possessed significant interferon γactivity and immune infiltration on immunohistochemistry. BN tumors were characterized by lower androgen receptor activity expression, lower immune infiltration, and enrichment with neuroendocrine expression patterns. Patients with LD tumors had less aggressive tumor characteristics and the longest time to metastasis after surgery. Only patients with BI tumors derived benefit from radiotherapy after surgery in terms of time to metastasis (hazard ratio [HR], 0.09; 95% CI, 0.01–0.71; n = 855). In a phase 3 trial that randomized patients with metastatic PCa to androgen deprivation with or without docetaxel (n = 108), only patients with LP tumors derived survival benefit from docetaxel (HR, 0.21; 95% CI, 0.09–0.51). Conclusions: With the use of expression profiles from over 100,000 tumors, a PSC was developed that identified four subtypes with distinct biological and clinical features. Plain language summary: Prostate cancer can behave in an indolent or aggressive manner and vary in how it responds to certain treatments. To differentiate prostate cancer on the basis of biological features, we developed a novel RNA signature by using data from over 100,000 prostate tumors—the largest data set of its kind. This signature can inform patients and physicians on tumor aggressiveness and susceptibilities to treatments to help personalize cancer management

Interaction between the microbiome and TP53 in human lung cancer.

BACKGROUND: Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort. RESULTS: Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas. CONCLUSIONS: The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection

Identification of Non-Pertechnetate Species In Hanford Tank Waste, Their Synthesis, Characterization, And Fundamental Chemistry

This proposal had three major goals: (1) develop capillary electrophoresis mass spectrometry as a characterization technique, (2) separate a non-pertechnetate fraction from a waste sample and identify the non-pertechnetate species in it by CEMS, and (3) synthesize and characterize bulk quantities of the identified non-pertechnetate species and study their ligand substitution and redox chemistry

How long do revised and multiply revised hip replacements last? A retrospective observational study of the National Joint Registry

Background Hip replacements are common and effective operations but patients that undergo this intervention are at risk of the replacements failing, requiring costly and often complex revision surgery with poorer outcomes than primary surgery. There is paucity of reliable data examining the treatment pathway for hip replacements over the life of the patient in terms of risk of revision and re-revisions. We aim to provide detailed information on the longevity of hip revision surgery. Methods We did a retrospective observational registry-based study of the National Joint Registry, using data on hip replacements from all participating hospitals in England and Wales, UK. We included data on all first revisions, with an identifiable primary procedure, with osteoarthritis as the sole indication for the original primary procedure. Kaplan-Meier estimates were used to determine the cumulative probability of revision and subsequent re-revision after primary hip replacement. Analyses were stratified by age and gender, and the influence of time from first to second revision on the risk of further revision was explored. Findings Between April 1, 2003, and Dec 31, 2019, there were 29 010 revision hip replacements with a linked primary episode. Revision rates of revision hip replacements were higher in patients younger than 55 years than in older age groups. After revision of primary total hip replacement, 21·3% (95% CI 18·6–24·4) of first revisions were revised again within 15 years, 22·3% (20·3–24·4) of second revisions were revised again within 7 years, and 22·3% (18·3–27·0) of third revisions were revised again within 3 years. After revision of hip resurfacing, 23·7% (95% CI 19·6–28·5) of these revisions were revised again within 15 years, 21·0% (17·0–25·8) of second revisions were revised again within 7 years, and 19·3% (11·9–30·4) of third revisions were revised again within 3 years. A shorter time between revision episodes was associated with earlier subsequent revision. Interpretation Younger patients are at an increased risk of multiple revisions. Patients who undergo a revision have a steadily increasing risk of further revision the more procedures they undergo, and each subsequent revision lasts for approximately half the time of the previous one. Although hip replacements are effective for improving pain and function and usually last a remarkably long time, if they are revised, successive revisions are progressively and markedly less successful