Theory, Epistemology and Critical Rural Sociology

Article originally published in International Journal of Sociology of Agriculture and FoodThis paper would like to provide an alternative to the Marx-Weber dichotomy which has recently emerged in rural sociological studies. It consists of the re-proposition of critical sociology as a mode of scientific investigation which, while remaining within the Marxian tradition, addresses many of the central concerns of Weberian scholarship. Though a merger between Marx and Weber is not proposed, it is assumed that a lack of knowledge of critical sociology has hampered further development of the theoretical debate in rural sociology. More importantly, this lack of knowledge has prevented the diffusion of the basic tenets of critical sociology among sociologists concerned with the study of agriculture and food, limiting their ability to inform empirical investigations and to instruct students.Sociolog

Thinking Globally About Universities and Extension: The Convergence of University-Based and Centralized Extension Systems in China

The U.S. university-based extension system model has been successful nationally, but not adopted globally. Various historical factors rendered the U.S. system a less attractive option for emerging post-WWII nations. However, current changes in education and extension landscapes are creating new opportunities for the globalization of U.S. Extension. Specifically, both the U.S. and Chinese extension systems now face the common challenge of delivering meaningful university-based extension under shifting conditions. This commonality creates opportunities for exploring long-term, synergistic university-based extension systems and potentially achieving associated benefits worldwide

A Deeper Look at DES Dwarf Galaxy Candidates: Grus I and Indus II

We present deep g- and r-band Magellan/Megacam photometry of two dwarf galaxy candidates discovered in the Dark Energy Survey (DES), Grus I and Indus II (DES J2038-4609). For the case of Grus I, we resolved the main sequence turn-off (MSTO) and similar to 2 mags below it. The MSTO can be seen at g(0) similar to 24 with a photometric uncertainty of 0.03 mag. We show Grus I to be consistent with an old, metal-poor (similar to 13.3 Gyr, [Fe/H] similar to -1.9) dwarf galaxy. We derive updated distance and structural parameters for Grus I using this deep, uniform, wide-field data set. We find an azimuthally-averaged halflight radius more than two times larger (similar to 151(-31)(+21) pc; similar to 4'. 16(-0.74)(+0.54)) and an absolute V-band magnitude similar to-4.1 that is similar to 1 magnitude brighter than previous studies. We obtain updated distance, ellipticity, and centroid parameters that are in agreement with other studies within uncertainties. Although our photometry of Indus II is similar to 2-3 magnitudes deeper than the DES Y1 public release, we find no coherent stellar population at its reported location. The original detection was located in an incomplete region of sky in the DES Y2Q1 data set and was flagged due to potential blue horizontal branch member stars. The best-fit isochrone parameters are physically inconsistent with both dwarf galaxies and globular clusters. We conclude that Indus II is likely a false positive, flagged due to a chance alignment of stars along the line of sight

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Incidence and outcomes of neonatal acute kidney injury (AWAKEN): a multicentre, multinational, observational cohort study

Background: Single-center studies suggest that neonatal acute kidney injury (AKI) is associated with poor outcomes. However, inferences regarding the association between AKI, mortality, and hospital length of stay are limited due to the small sample size of those studies. In order to determine whether neonatal AKI is independently associated with increased mortality and longer hospital stay, we analyzed the Assessment of Worldwide Acute Kidney Epidemiology in Neonates (AWAKEN) database. Methods: All neonates admitted to 24 participating neonatal intensive care units from four countries (Australia, Canada, India, United States) between January 1 and March 31, 2014, were screened. Of 4273 neonates screened, 2022 (47·3%) met study criteria. Exclusion criteria included: no intravenous fluids ≥48 hours, admission ≥14 days of life, congenital heart disease requiring surgical repair at <7 days of life, lethal chromosomal anomaly, death within 48 hours, inability to determine AKI status or severe congenital kidney abnormalities. AKI was defined using a standardized definition -i.e., serum creatinine rise of ≥0.3 mg/dL (26.5 mcmol/L) or ≥50% from previous lowest value, and/or if urine output was <1 mL/kg/h on postnatal days 2 to 7. Findings: Incidence of AKI was 605/2022 (29·9%). Rates varied by gestational age groups (i.e., ≥22 to <29 weeks =47·9%; ≥29 to <36 weeks =18·3%; and ≥36 weeks =36·7%). Even after adjusting for multiple potential confounding factors, infants with AKI had higher mortality compared to those without AKI [(59/605 (9·7%) vs. 20/1417 (1·4%); p< 0.001; adjusted OR=4·6 (95% CI=2·5-8·3); p=<0·0001], and longer hospital stay [adjusted parameter estimate 8·8 days (95% CI=6·1-11·5); p<0·0001]. Interpretation: Neonatal AKI is a common and independent risk factor for mortality and longer hospital stay. These data suggest that neonates may be impacted by AKI in a manner similar to pediatric and adult patients