From Food and Fuel to Farms and Flocks: The Integration of Plant and Animal Remains in the Study of the Agropastoral Economy at Gordion, Turkey

The site of Gordion, Turkey, provides a case study of the integrated use of archaeobiological data. Associations between botanical and faunal remains suggest a continuum of land‐use practices. At one end, high ratios of the seeds of wild plants versus cultivated cereal grains (calculated as count/weight) and high proportions of the bones of sheep, goat, and deer are signatures of a subsistence economy focused on pastoral production. At the other, low wild/cereal ratios along with high proportions of the bones of cattle, pig, and hare indicate an economy more focused on agriculture. Based on the millennium‐long sequence analyzed, the most sustainable land use around the ancient settlement emphasized pastoral production; only during the wealthy Middle Phrygian period did high population support greater reliance on agriculture

Excavation and Survey in the Jabbul Plain, Western Syria: The Umm el-Marra Project 1996-1997

The 1996 and 1997 seasons of the Hopkins-Amsterdam project in the Jabbul plain, western Syria, have generated new results on Bronze Age urbanism at Tell Umm el- Marra and elucidated longer-term settlement patterns in the Jabbul region. Excavation results have documented the foundation of Umm el-Marra as a regional center in the Early Bronze Age, provided new data on a period of decentralization in Middle Bronze I, and supplied evidence of the regeneration of urbanism in MB II. Faunal and archaeobotanical analysis broaden our understanding of these developments, attesting to an economy overwhelmingly dependent on the steppe environment, with an emphasis on large-scale onager hunting in MB II. Finally, a regional survey provides data on long-term demographic and socioeconomic trends, furnishing an expansive time range and spatial context for our under- standing of developmental patterns in the region. The survey results supply new information on the limits of the Uruk expansion, cycles of Bronze Age urbanization, changing patterns of steppe exploitation, and demo- graphic and agricultural extensification in the Byzantine and Early Islamic periods

Ductal carcinoma in situ of the breast (DCIS) with heterogeneity of nuclear grade: prognostic effects of quantitative nuclear assessment

<p>Abstract</p> <p>Background</p> <p>Previously, 50% of patients with breast ductal carcinoma <it>in situ (</it>DCIS) had more than one nuclear grade, and neither worst nor predominant nuclear grade was significantly associated with development of invasive carcinoma. Here, we used image analysis in addition to histologic evaluation to determine if quantification of nuclear features could provide additional prognostic information and hence impact prognostic assessments.</p> <p>Methods</p> <p>Nuclear image features were extracted from about 200 nuclei of each of 80 patients with DCIS who underwent lumpectomy alone, and received no adjuvant systemic therapy. Nuclear images were obtained from 20 representative nuclei per duct, from each of a group of 5 ducts, in two separate fields, for 10 ducts. Reproducibility of image analysis features was determined, as was the ability of features to discriminate between nuclear grades. Patient information was available about clinical factors (age and method of DCIS detection), pathologic factors (DCIS size, nuclear grade, margin size, and amount of parenchymal involvement), and 39 image features (morphology, densitometry, and texture). The prognostic effects of these factors and features on the development of invasive breast cancer were examined with Cox step-wise multivariate regression.</p> <p>Results</p> <p>Duplicate measurements were similar for 89.7% to 97.4% of assessed image features. For the pooled assessment with ~200 nuclei per patient, a discriminant function with one densitometric and two texture features was significantly (p < 0.001) associated with nuclear grading, and provided 78.8% correct jackknifed classification of a patient's nuclear grade. In multivariate assessments, image analysis nuclear features had significant prognostic associations (p ≤ 0.05) with the development of invasive breast cancer. Texture (difference entropy, p < 0.001; contrast, p < 0.001; peak transition probability, p = 0.01), densitometry (range density, p = 0.004), and measured margin (p = 0.05) were associated with development of invasive disease for the pooled data across all ducts.</p> <p>Conclusion</p> <p>Image analysis provided reproducible assessments of nuclear features which quantitated differences in nuclear grading for patients. Quantitative nuclear image features indicated prognostically significant differences in DCIS, and may contribute additional information to prognostic assessments of which patients are likely to develop invasive disease.</p

Effect of Quantitative Nuclear Image Features on Recurrence of Ductal Carcinoma In Situ (DCIS) of the Breast

BACKGROUND: Nuclear grade has been associated with breast DCIS recurrence and progression to invasive carcinoma; however, our previous study of a cohort of patients with breast DCIS did not find such an association with outcome. Fifty percent of patients had heterogeneous DCIS with more than one nuclear grade. The aim of the current study was to investigate the effect of quantitative nuclear features assessed with digital image analysis on ipsilateral DCIS recurrence.CONCLUSION: Analysis of nuclear features measured by image cytometry may contribute to the classification and prognosis of breast DCIS patients with more than one nuclear grade.Author manuscript. Published in final edited form as: Cancer Informatics 2008:4 99–109.The final published version of this article is located at: http://la-press.com/article.php?article_id=583NIH U56 CA113004; to David E. AxelrodThis work was funded by the New Jersey Commission for Cancer Research 1076-CCRS0, the National Institutes of Health U56 CA113004, the Hyde and Watson Foundation, the Busch Memorial Fund, and the E.B. Fish Research Fund.NJ Commission on Cancer Research 1076-CCR-SO; to David E. Axelro

Engaging with assessment: increasing student engagement through continuous assessment

Student engagement is intrinsically linked to two important metrics in learning: student satisfaction and the quality of the student experience. One of the ways that engagement can be influenced is through careful curriculum design. Using the knowledge that many students are ‘assessment-driven’ a low stakes continuous weekly summative e-assessment was introduced to a module. The impact this had on student engagement was measured by studying student activity within the module virtual learning environment (VLE). It was found that introduction of the e-assessments led to a significant increase in VLE activity compared to the VLE activity in that module the previous year, and also compared to the VLE activity of two other modules studied by the same student cohort. As many institutions move towards greater blended or online deliveries it will become more important to ensure that VLEs encourage high levels of student engagement in order to maintain or enhance the student experience. Keywords : continuous assessment, learning analytics, student engagement, virtual learning environment

Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma.

Almost all genomic studies of breast cancer have focused on well-established tumours because it is technically challenging to study the earliest mutational events occurring in human breast epithelial cells. To address this we created a unique dataset of epithelial samples ductoscopically obtained from ducts leading to breast carcinomas and matched samples from ducts on the opposite side of the nipple. Here, we demonstrate that perturbations in mRNA abundance, with increasing proximity to tumour, cannot be explained by copy number aberrations. Rather, we find a possibility of field cancerization surrounding the primary tumour by constructing a classifier that evaluates where epithelial samples were obtained relative to a tumour (cross-validated micro-averaged AUC = 0.74). We implement a spectral co-clustering algorithm to define biclusters. Relating to over-represented bicluster pathways, we further validate two genes with tissue microarrays and in vitro experiments. We highlight evidence suggesting that bicluster perturbation occurs early in tumour development

Experimental transmission of Stony Coral Tissue Loss Disease results in differential microbial responses within coral mucus and tissue

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Huntley, N., Brandt, M., Becker, C., Miller, C., Meiling, S., Correa, A., Holstein, D., Muller, E., Mydlarz, L., Smith, T., & Apprill, A. Experimental transmission of Stony Coral Tissue Loss Disease results in differential microbial responses within coral mucus and tissue. ISME Communications, 2(1), (2022): 46, https://doi.org/10.1038/s43705-022-00126-3.Stony coral tissue loss disease (SCTLD) is a widespread and deadly disease that affects nearly half of Caribbean coral species. To understand the microbial community response to this disease, we performed a disease transmission experiment on US Virgin Island (USVI) corals, exposing six species of coral with varying susceptibility to SCTLD. The microbial community of the surface mucus and tissue layers were examined separately using a small subunit ribosomal RNA gene-based sequencing approach, and data were analyzed to identify microbial community shifts following disease acquisition, potential causative pathogens, as well as compare microbiota composition to field-based corals from the USVI and Florida outbreaks. While all species displayed similar microbiome composition with disease acquisition, microbiome similarity patterns differed by both species and mucus or tissue microhabitat. Further, disease exposed but not lesioned corals harbored a mucus microbial community similar to those showing disease signs, suggesting that mucus may serve as an early warning detection for the onset of SCTLD. Like other SCTLD studies in Florida, Rhodobacteraceae, Arcobacteraceae, Desulfovibrionaceae, Peptostreptococcaceae, Fusibacter, Marinifilaceae, and Vibrionaceae dominated diseased corals. This study demonstrates the differential response of the mucus and tissue microorganisms to SCTLD and suggests that mucus microorganisms may be diagnostic for early disease exposure.This work was funded by an International Coral Reef Society student grant to N.H., National Science Foundation (NSF) VI EPSCoR 0814417 and 1946412 and NSF (Biological Oceanography) award numbers 1928753 to MEB and TBS, 1928609 to AMSC, 1928817 to EMM, 19228771 to LDM, 1927277 to DMH as well as 1928761 and 1938112 to AA, NSF EEID award number 2109622 to MEB, AA, LDM, and AMSC, and a NOAA OAR Cooperative Institutes award to AA (#NA19OAR4320074). Samples were collected under permit #DFW19057U authorized by the Department of Planning and Natural Resources Coastal Zone Management

"Can't live willingly": A thematic synthesis of qualitative evidence exploring how early marriage and early pregnancy affect experiences of pregnancy in South Asia.

In South Asia, early marriage has been associated with a range of adverse outcomes during pregnancy and infancy. This may partly be explained by early marriage leading to a younger maternal age, however it remains unclear which other factors are involved. This review aimed to synthesise the qualitative evidence on experiences of pregnancy following early marriage or early pregnancy in South Asia, to inform our understanding of the mechanisms between early marriage and adverse pregnancy outcomes. We searched MEDLINE, EMBASE, Scopus, Global Index Medicus, CINAHL, PsycINFO, Web of Science, and grey literature on 29/11/2022 to identify papers on experiences of pregnancy among those who married or became pregnant early in South Asia (PROSPERO registration number: CRD42022304336, funded by an MRC doctoral training grant). Seventy-nine papers from six countries were included after screening. We appraised study quality using an adapted version of the Critical Appraisal Skills Programme tool for qualitative research. Reporting of reflexivity and theoretical underpinnings was poor. We synthesised findings thematically, presenting themes alongside illustrative quotes. We categorised poor pregnancy experiences into: care-seeking challenges, mental health difficulties, and poor nutritional status. We identified eight inter-connected themes: restrictive social hierarchies within households, earning social position, disrupted education, social isolation, increased likelihood of and vulnerability to abuse, shaming of pregnant women, normalisation of risk among younger women, and burdensome workloads. Socioeconomic position and caste/ethnic group also intersected with early marriage to shape experiences during pregnancy. While we found differences between regions, the heterogeneity of the included studies limits our ability to draw conclusions across regions. Pregnancy experiences are largely determined by social hierarchies and the quality of relationships within and outside of the household. These factors limit the potential for individual factors, such as education and empowerment, to improve experiences of pregnancy for girls married early

Modeling regional-scale wildland fire emissions with the wildland fire emissions information system

As carbon modeling tools become more comprehensive, spatial data are needed to improve quantitative maps of carbon emissions from fire. The Wildland Fire Emissions Information System (WFEIS) provides mapped estimates of carbon emissions from historical forest fires in the United States through a web browser. WFEIS improves access to data and provides a consistent approach to estimating emissions at landscape, regional, and continental scales. The system taps into data and tools developed by the U.S. Forest Service to describe fuels, fuel loadings, and fuel consumption and merges information from the U.S. Geological Survey (USGS) and National Aeronautics and Space Administration on fire location and timing. Currently, WFEIS provides web access to Moderate Resolution Imaging Spectroradiometer (MODIS) burned area for North America and U.S. fire-perimeter maps from the Monitoring Trends in Burn Severity products from the USGS, overlays them on 1-km fuel maps for the United States, and calculates fuel consumption and emissions with an open-source version of the Consume model. Mapped fuel moisture is derived from daily meteorological data from remote automated weather stations. In addition to tabular output results, WFEIS produces multiple vector and raster formats. This paper provides an overview of the WFEIS system, including the web-based system functionality and datasets used for emissions estimates. WFEIS operates on the web and is built using open-source software components that work with open international standards such as keyhole markup language (KML). Examples of emissions outputs from WFEIS are presented showing that the system provides results that vary widely across the many ecosystems of North America and are consistent with previous emissions modeling estimates and products