The Hyper Suprime-Cam Software Pipeline

In this paper, we describe the optical imaging data processing pipeline developed for the Subaru Telescope's Hyper Suprime-Cam (HSC) instrument. The HSC Pipeline builds on the prototype pipeline being developed by the Large Synoptic Survey Telescope's Data Management system, adding customizations for HSC, large-scale processing capabilities, and novel algorithms that have since been reincorporated into the LSST codebase. While designed primarily to reduce HSC Subaru Strategic Program (SSP) data, it is also the recommended pipeline for reducing general-observer HSC data. The HSC pipeline includes high level processing steps that generate coadded images and science-ready catalogs as well as low-level detrending and image characterizations.Comment: 39 pages, 21 figures, 2 tables. Submitted to Publications of the Astronomical Society of Japa

New Methods for ALK Status Diagnosis in Non–Small-Cell Lung Cancer: An Improved ALK Immunohistochemical Assay and a New, Brightfield, Dual ALK IHC–In Situ Hybridization Assay

Introduction:The demonstration of anaplastic lymphoma kinase (ALK) positivity in non–small-cell lung cancer (NSCLC) has been hindered by the technical complexity and interpretative challenges of fluorescence in situ hybridization methods for detection of ALK gene rearrangement and by the inadequate sensitivity of existing immunohistochemistry (IHC) methods for ALK protein detection. In this study, we sought to increase the sensitivity of ALK IHC detection and to develop a brightfield assay for concurrent detection of ALK protein expression and ALK gene rearrangement.Methods:We developed a horseradish peroxidase–based IHC detection system using the novel, nonendogenous hapten 3-hydroxy-2-quinoxaline (HQ) and tyramide. We also developed a dual gene protein ALK assay combining a brightfield break-apart in situ hybridization ALK assay with another sensitive IHC method using the novel, nonendogenous hapten 5-nitro-3-pyrazole. We examined the sensitivity and accuracy of these methods using surgically resected NSCLC cases examined with ALK fluorescence in situ hybridization.Results:The new HQ-tyramide IHC detection system offered readily interpretable staining with substantially greater sensitivity than conventional ALK IHC, and produced heterogeneous and homogeneous patterns of ALK protein staining among ALK-positive NSCLC surgical cases. The new 5-nitro-3-pyrazole–based IHC detection system was similar in ALK detection sensitivity to the HQ-tyramide IHC system and was compatible with the brightfield in situ hybridization assay.Conclusion:The new HQ-tyramide IHC reagent system allows more sensitive assessment of ALK protein status in NSCLC cases. The new ALK gene-protein assay allows the concurrent visualization of ALK gene and ALK protein status in single cells, allowing more accurate ALK status determination even in heterogeneous specimens

Acute WNT signalling activation perturbs differentiation within the adult stomach and rapidly leads to tumour formation

A role for WNT signalling in gastric carcinogenesis has been suggested due to two major observations. First, patients with germline mutations in adenomatous polyposis coli (APC) are susceptible to stomach polyps and second, in gastric cancer, WNT activation confers a poor prognosis. However, the functional significance of deregulated WNT signalling in gastric homoeostasis and cancer is still unclear. In this study we have addressed this by investigating the immediate effects of WNT signalling activation within the stomach epithelium. We have specifically activated the WNT signalling pathway within the mouse adult gastric epithelium via deletion of either glycogen synthase kinase 3 (GSK3) or APC or via expression of a constitutively active β-catenin protein. WNT pathway deregulation dramatically affects stomach homoeostasis at very short latencies. In the corpus, there is rapid loss of parietal cells with fundic gland polyp (FGP) formation and adenomatous change, which are similar to those observed in familial adenomatous polyposis. In the antrum, adenomas occur from 4 days post-WNT activation. Taken together, these data show a pivotal role for WNT signalling in gastric homoeostasis, FGP formation and adenomagenesis. Loss of the parietal cell population and corresponding FGP formation, an early event in gastric carcinogenesis, as well as antral adenoma formation are immediate effects of nuclear β-catenin translocation and WNT target gene expression. Furthermore, our inducible murine model will permit a better understanding of the molecular changes required to drive tumourigenesis in the stomach

Nature meets nurture: molecular genetics of gastric cancer

The immensity of genes and molecules implicated in gastric carcinogenesis is overwhelming and the relevant importance of some of these molecules is too often unclear. This review serves to bring us up-to-date with the latest findings as well as to look at the larger picture in terms of how to tackle the problem of solving this multi-piece puzzle. In this review, the environmental nurturing of intestinal cancer is discussed, beginning with epidemiology (known causative factors for inducing molecular change), an update of H. pylori research, including the role of inflammation and stem cells in premalignant lesions. The role of E-cadherin in the nature (genotype) of diffuse gastric cancer is highlighted, and finally the ever growing discipline of SNP analysis (including IL1B) is discussed

Gastric adenocarcinoma trends in the central region of Rio Grande do Sul (Southern Brazil): what has changed in 25 years?

CONTEXT: Gastric cancer is the fourth most common malignancy in the world. Its incidence varies greatly by geographic region. The highest rate is in Eastern Asia, mainly in Japan and China. In Brazil, gastric cancer is the third most common cancer in males and the fifth most common cancer in females. Rio Grande do Sul state, in Southern Brazil, has similar figures. The main histological type of gastric cancer is adenocarcinoma. OBJECTIVE: To assess the trends of this cancer over 25 years in a reference center in central Rio Grande do Sul. METHODS: We reviewed the records of upper gastrointestinal endoscopies performed at the University Hospital of Santa Maria, RS, between 1986 and 2010. We evaluated the incidence, age and gender distribution, anatomical subsite and histological subtype of gastric cancer throughout this 25-year period. RESULTS: We identified histologically confirmed primary gastric adenocarcinoma in 335 (1.6%) of the 20,521 patients who underwent upper gastrointestinal endoscopy during the study period. The mean age of patients was 62.4 (± 13.0) years, and 67.8% were male (a male: female ratio of 2.0:1). Cardia cancer accounted for 14.3% of the cases, and non-cardia cancer accounted for 85.7%. According to Lauren's classification, 48.1% were intestinal subtype and 40.9% were diffuse subtype. There were no differences in mean age or gender distribution by anatomical location or histological subtype. There was also no difference in the proportions of histological subtypes by anatomical location. Over the 25-year period, there was no change in the anatomical distribution of tumors, but there was a significant decrease in the intestinal subtype and a steady increase in the diffuse subtype (P = 0.02). The subset of 39 patients (11.6%) who presented at < 45 years of age was more likely to be female and to have tumors of the diffuse subtype than was the total series of patients. CONCLUSIONS: Over this 25-year period, there were no significant trends in age, gender distribution, or the proportions of cardia and non-cardia gastric adenocarcinomas in this series of patients from Southern Brazil. There was a significant decrease in the intestinal subtype and a steady increase in the diffuse subtype of this malignancy. In patients under 45 years old, gastric cancer was more frequent in women, and the diffuse subtype predominated

Brain distribution of carboxy terminus of Hsc70-interacting protein (CHIP) and its nuclear translocation in cultured cortical neurons following heat stress or oxygen–glucose deprivation

Carboxy terminus of Hsc70-interacting protein (CHIP) is thought to be a cytoprotective protein with protein quality control roles in neurodegenerative diseases and myocardial ischemia. This study describes the localization of CHIP expression in normal rodent brain and the early CHIP response in primary cultures of cortical neurons following ischemic stress models: heat stress (HS) and oxygen–glucose deprivation (OGD). CHIP was highly expressed throughout the brain, predominantly in neurons. The staining pattern was primarily cytoplasmic, although small amounts were seen in the nucleus. More intense nuclear staining was observed in primary cultured neurons which increased with stress. Nuclear accumulation of CHIP occurred within 5–10 min of HS and decreased to baseline levels or lower by 30–60 min. Decrease in nuclear CHIP at 30–60 min of HS was associated with a sharp increase in delayed cell death. While no changes in cytoplasmic CHIP were observed immediately following OGD, nuclear levels of CHIP increased slightly in response to OGD durations of 30 to 240 min. OGD-induced increases in nuclear CHIP decreased slowly during post-ischemic recovery. Nuclear CHIP decreased earlier in recovery following 120 min of OGD (4 h) than 30 min of OGD (12 h). Significant cell death first appeared between 12 and 24 h after OGD, again suggesting that delayed cell death follows closely behind the disappearance of nuclear CHIP. The ability of CHIP to translocate to and accumulate in the nucleus may be a limiting variable that determines how effectively cells respond to external stressors to facilitate cell survival. Using primary neuronal cell cultures, we were able to demonstrate rapid translocation of CHIP to the nucleus within minutes of heat stress and oxygen–glucose deprivation. An inverse relationship between nuclear CHIP and delayed cell death at 24 h suggests that the decrease in nuclear CHIP following extreme stress is linked to delayed cell death. Our findings of acute changes in subcellular localization of CHIP in response to cellular stress suggest that cellular changes that occur shortly after exposure to stress ultimately impact on the capacity and capability of a cell to recover and survive

Dynamic glucocorticoid-dependent regulation of Sgk1 expression in oligodendrocytes of adult male rat brain by acute stress and time of day

Recent studies support plasticity in adult brain white matter structure and myelination in response to various experiential factors. One possible contributor to this plasticity may be activity-dependent modulation of serum- and glucocorticoid-inducible kinase 1 (Sgk1) expression in oligodendrocytes. We examined whether Sgk1 expression in adult rat brain white matter is increased by acute stress-induced elevations in endogenous corticosterone and whether it fluctuates with diurnal variations in corticosterone. We observed rapid increases (within 30 min) in Sgk1 mRNA in the corpus callosum in response to acute stress, as well as large increases at the beginning of the rat's active period (the time of peak corticosterone secretion). These increases were absent in adrenalectomized rats. Corticosterone treatment of adrenalectomized rats also rapidly increased corpus callosum Sgk1 mRNA. The majority of Sgk1 mRNA in corpus callosum was co-localized with myelin basic protein mRNA, suggesting that mature oligodendrocytes respond dynamically to acute stress and circadian rhythms. The regulation of Sgk1 expression by acute stress and time of day was selective for white matter, with limited alteration of Sgk1 expression by these factors in hippocampus and somatosensory cortex. These results indicate a unique sensitivity of oligodendrocyte Sgk1 expression to activity-dependent fluctuations in corticosterone hormone secretion, and raises the prospect that hypothalamic-pituitary-adrenal axis dysregulation or glucocorticoid pharmacotherapy may compromise the normal activity-dependent interactions between oligodendrocytes and neurons

Allostery in Recombinant Soluble Guanylyl Cyclase from Manduca sexta*

Soluble guanylyl/guanylate cyclase (sGC), the primary biological receptor for nitric oxide, is required for proper development and health in all animals. We have expressed heterodimeric full-length and N-terminal fragments of Manduca sexta sGC in Escherichia coli, the first time this has been accomplished for any sGC, and have performed the first functional analyses of an insect sGC. Manduca sGC behaves much like its mammalian counterparts, displaying a 170-fold stimulation by NO and sensitivity to compound YC-1. YC-1 reduces the NO and CO off-rates for the ∼100-kDa N-terminal heterodimeric fragment and increases the CO affinity by ∼50-fold to 1.7 μm. Binding of NO leads to a transient six-coordinate intermediate, followed by release of the proximal histidine to yield a five-coordinate nitrosyl complex (k6-5 = 12.8 s-1). The conversion rate is insensitive to nucleotides, YC-1, and changes in NO concentration up to ∼30 μm. NO release is biphasic in the absence of YC-1 (koff1 = 0.10 s-1 and koff2 = 0.0015 s-1); binding of YC-1 eliminates the fast phase but has little effect on the slower phase. Our data are consistent with a model for allosteric activation in which sGC undergoes a simple switch between two conformations, with an open or a closed heme pocket, integrating the influence of numerous effectors to give the final catalytic rate. Importantly, YC-1 binding occurs in the N-terminal two-thirds of the protein. Homology modeling and mutagenesis experiments suggest the presence of an H-NOX domain in the α subunit with importance for heme binding