Reproductive anatomy of adult female emus (Dromaius novaehollandiae)

The following investigation was conducted in order to describe the morphology of the female reproductive system of an adult, two year old physically mature, but reproductively inactive female emu (Dromaius novaehollandiae). The dissections focused on the morphology of the reproductive tract of the female emu including the vasculature and the innervation of the reproductive organs. For this investigation, five female emus (Dromaius novaehollandiae) were obtained. Three were two years old, physically mature, but reproductively inactive. These emus were anesthetized and an endoscopic exam was done and a video recorded. Two were yearlings and not physically or reproductively mature. The emus were prepared for embalming via intravascular injection of 10% formalin and submerged in a 5% formalin solution. Two days after fixation, colored latex was injected into the arteries and veins to aid in the visualization and dissection of the vasculature of the reproductive tract. The reproductive tract of the adult female emu consisted of an ovary and oviduct situated on the left side of the abdominal cavity. The left ovary was a dark brownish-black color with the ventral surface of the ovary covered in follicles. The ovary was medial to the spleen and associated with the ventral surface of the cranial and middle lobes of the left kidney. The left oviduct was a nearly straight tube that extended from the cranial extent of the left ilium (which corresponded to the thoracolumbar junction) to the caudal border of the left pubic bone. The oviduct was divided into five regions from cranial to caudal based on the pattern and orientation of the mucosal folds. The regions of the oviduct were the infundibulum, the magnum, the isthmus, the uterus and the vagina. The arterial supply of the ovary and oviduct was accomplished by the ovarian artery, the cranial oviductal artery, the accessory cranial oviductal artery, the middle oviductal artery, the caudal oviductal artery and the medial and lateral vaginal arteries. These arteries supplied various regions of the oviduct and were branches of the left cranial renal artery, the left pubic artery, the left middle renal artery and the left pudendal artery. The left ovary was drained by a single ovarian vein which joined the left adrenal vein and subsequently emptied into the left side of the caudal vena cava. The veins of the oviduct were satellites of the arteries that supplied the oviduct and also drained into the caudal vena cava. The main innervation of the reproductive tract was via a large ovarian nerve plexus which emerged laterally from the left adrenal gland. Overall the anatomy of the ovary and oviduct of the female emu was similar to the domestic fowl. The ovary was located on the left side of the abdomen, but the color, shape and size of the ovary and the follicles varied in the emu from that of the domestic fowl. Differences in the oviduct were observed in the pattern and orientation of the mucosal folds in the magnum, uterus and the vagina in the emu and from the domestic fowl. The pattern of vasculature was similar in both except for the presence of the accessory cranial oviductal artery, the anastomosis of the caudal oviductal artery with the dorsal uterine artery and the presence of medial and lateral vaginal arteries in the emu

Comparative Anatomy of the Lower Respiratory Tract of the Gray Short-tailed Opossum (Monodelphis domestica) and North American Opossum (Didelphis virginiana)

The present study describes the lower respiratory tract anatomy of the gray short-tailed opossum (Monodelphis domestica) and North American opossum (Didelphis virginiana). The trachea of the gray short-tailed opossum consists of 25 c-shaped tracheal cartilages. The trachea of the North American opossum consists of 28 c-shaped cartilages. The right lung of both species is separated into cranial, middle, caudal and accessory lobes by interlobar fissures. The left lung consists of unseparated cranial and caudal lobes. The right and left pulmonary arteries of the gray short-tailed and North American opossums divide into pulmonary lobar arteries. The pulmonary lobar veins join to form pulmonary veins. In the gray short-tailed opossum, the pulmonary lobar veins join to form a right and left pulmonary vein which join to form a common pulmonary venous trunk. In the North American opossum, a similar pattern occurs however the common pulmonary venous trunk is formed from three pulmonary veins (right, left and middle). Vascularization of the lung parenchyma is via the bronchial artery, a branch of the bronchoesophageal artery. Right and left bronchial branches course along the dorsal surface of the principal bronchi toward the hilus of the lung. In both species, the left bronchial branch anastomoses with a mediastinal artery originating from the aorta. Cranial deep cervical, cranial mediastinal and tracheobronchial lymph nodes drain the lower respiratory tract of both species. Sympathetic innervation to the lungs of the opossums comes from the sympathetic trunks as thoracic splanchnic nerves. Parasympathetic innervation to the lungs is via branches from the vagus nerves. The trachea and principal bronchi of the gray short-tailed opossum are lined by pseudostratified ciliated columnar epithelium. Bronchial cartilages are irregular, shaped plates and localized to the extrpulmonary portion of the principal bronchus. The secondary and tertiary bronchi and primary and secondary bronchioles are lined by simple ciliated columnar epithelium. The terminal bronchioles and proximal portion of the respiratory bronchioles are lined by simple ciliated cuboidal epithelium. The distal portion of the respiratory bronchioles and the alveolar ducts are lined by simple squamous epithelium. The alveoli are lined by type I and II pneumocytes

γδ T Cells Are Reduced and Rendered Unresponsive by Hyperglycemia and Chronic TNFα in Mouse Models of Obesity and Metabolic Disease

Epithelial cells provide an initial line of defense against damage and pathogens in barrier tissues such as the skin; however this balance is disrupted in obesity and metabolic disease. Skin γδ T cells recognize epithelial damage, and release cytokines and growth factors that facilitate wound repair. We report here that hyperglycemia results in impaired skin γδ T cell proliferation due to altered STAT5 signaling, ultimately resulting in half the number of γδ T cells populating the epidermis. Skin γδ T cells that overcome this hyperglycemic state are unresponsive to epithelial cell damage due to chronic inflammatory mediators, including TNFα. Cytokine and growth factor production at the site of tissue damage was partially restored by administering neutralizing TNFα antibodies in vivo. Thus, metabolic disease negatively impacts homeostasis and functionality of skin γδ T cells, rendering host defense mechanisms vulnerable to injury and infection

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

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

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large-scale structure. BOSS uses 1.5 million luminous galaxies as faint as i = 19.9 over 10,000 deg(2) to measure BAO to redshifts z < 0.7. Observations of neutral hydrogen in the Ly alpha forest in more than 150,000 quasar spectra (g < 22) will constrain BAO over the redshift range 2.15 < z < 3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Ly alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance d(A) to an accuracy of 1.0% at redshifts z = 0.3 and z = 0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Ly alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D-A(z) and H-1(z) parameters to an accuracy of 1.9% at z similar to 2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS