A strategy for the measurement of CO2 distribution in the stratosphere

Abstract. In this study we introduce a new strategy for the measurement of CO2 distribution in the stratosphere. The proposed experiment is based on an orbiting limb sounder that measures the atmospheric emission within both the thermal infrared (TIR) and far-infrared (FIR) regions. The idea is to exploit the contribution of the pure rotational transitions of molecular oxygen in the FIR to determine the atmospheric fields of temperature and pressure that are necessary to retrieve the distribution of CO2 from its rovibrational transitions in the TIR. The instrument envisaged to test the new strategy is a Fourier transform spectrometer with two output ports hosting a FIR detector devoted to measuring the O2 transitions and a TIR detector devoted to measure the CO2 transitions. Instrumental and observational parameters of the proposed experiment have been defined by exploiting the heritage of both previous studies and operational limb sounders. The performance of the experiment has been assessed with two-dimensional (2-D) retrievals on simulated observations along a full orbit. For this purpose, optimal spectral intervals have been defined using a validated selection algorithm. Both precision and spatial resolution of the obtained CO2 distributions have been taken into account in the results–evaluation process. We show that the O2 spectral features significantly contribute to the performance of CO2 retrievals and that the proposed experiment can determine 2-D distributions of the CO2 volume mixing ratio with precisions of the order of 1 ppmv in the 10–50 km altitude range. The error budget, estimated for the test case of an ideal instrument and neglecting the spectroscopic errors, indicates that, in the 10–50 km altitude range, the total error of the CO2 fields is set by the random component. This is also the case at higher altitudes, provided the retrieval system is able to model the non-local thermal equilibrium conditions of the atmosphere. The best performance is obtained at altitudes between 20 and 50 km, where the vertical resolution ranges from 3 to 5 km, and the horizontal resolution is of the order of 300–350 km depending on latitude

Phosgene in the UTLS: seasonal and latitudinal variations from MIPAS observations

Abstract. The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) is a Fourier transform spectrometer that measured mid-infrared atmospheric limb emission spectra from July 2002 to April 2012 on board the polar-orbiting satellite ENVISAT. We have used MIPAS data to study the latitudinal variations of phosgene (COCl2 or carbonyl chloride) and, for the first time, its seasonal variation in the upper troposphere/lower stratosphere region (UTLS). Retrievals of phosgene were made using the 830–860 cm−1 region, corresponding to the ν5 bands of COCl2. Unfortunately, in that region, the ν4 band of CFC-11, which is much stronger than COCl2 ν5, hides the phosgene emission. In order to evaluate seasonality and latitudinal distribution of phosgene we have analysed all the measurements made by MIPAS on days 18 and 20 of each month of 2008 with the optimized retrieval model (ORM) recently upgraded with the multi-target retrieval technique and with the optimal estimation functionality to apply external constraints to the state vector. Average seasonal profiles of phosgene show an evident latitudinal variability with the largest values observed in the tropical regions (maximum  ≈  35 parts per trillion by volume (pptv) at about 300 hPa). In the midlatitude and polar regions, the volume mixing ratio (VMR) values do not exceed 30 pptv and the vertical distributions are less peaked. Our analysis highlights that COCl2 seasonal variability is fairly low, apart from the polar regions

Measurement of the isotopic ratio distribution of HD(16)O and H(2)(16)O in the 20-38 km altitude range from far-infrared spectra

The altitude distribution of the isotopic ratio between HD(16)O and H(2) (16)O in the stratosphere is derived by retrieving the mixing ratio profiles (from 20 km to 38 km of altitude) of the two isotopic species from far‐infrared emission spectra. The measurements were made with a balloon‐borne Fourier Transform Spectrometer capable of 0.0025 cm(−1) spectral resolution during the IBEX 92 campaign. The retrievals were carried out using the global‐fit procedure on a statistically significant number of spectra for each isotope, in the 40–75 cm(−1) spectral region. This measurement determines the D/H ratio in stratospheric water over an altitude range larger than that of previous measurements. The value of the HD(16)O/H(2) (16)O ratio, normalized to the standard value, ranges from 0.4 to 0.5 (with a 10% random error) in the altitude range studied and is in good agreement with the values previously measured

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

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

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

Pdx1 Is Post-Translationally Modified In vivo and Serine 61 Is the Principal Site of Phosphorylation

Maintaining sufficient levels of Pdx1 activity is a prerequisite for proper regulation of blood glucose homeostasis and beta cell function. Mice that are haploinsufficient for Pdx1 display impaired glucose tolerance and lack the ability to increase beta cell mass in response to decreased insulin signaling. Several studies have shown that post-translational modifications are regulating Pdx1 activity through intracellular localization and binding to co-factors. Understanding the signaling cues converging on Pdx1 and modulating its activity is therefore an attractive approach in diabetes treatment. We employed a novel technique called Nanofluidic Proteomic Immunoassay to characterize the post-translational profile of Pdx1. Following isoelectric focusing in nano-capillaries, this technology relies on a pan specific antibody for detection and it therefore allows the relative abundance of differently charged protein species to be examined simultaneously. In all eukaryotic cells tested we find that the Pdx1 protein separates into four distinct peaks whereas Pdx1 protein from bacteria only produces one peak. Of the four peaks in eukaryotic cells we correlate one of them to a phosphorylation Using alanine scanning and mass spectrometry we map this phosphorylation to serine 61 in both Min6 cells and in exogenous Pdx1 over-expressed in HEK293 cells. A single phosphorylation is also present in cultured islets but it remains unaffected by changes in glucose levels. It is present during embryogenesis but is not required for pancreas development

Pattern of Relapse and Treatment Response in WNT- Activated Medulloblastoma

Over the past decade, wingless-activated (WNT) medulloblastoma has been identified as a candidate for therapy de-escalation based on excellent survival; however, a paucity of relapses has precluded additional analyses of markers of relapse. To address this gap in knowledge, an international cohort of 93 molecularly confirmed WNT MB was assembled, where 5-year progression-free survival is 0.84 (95%, 0.763-0.925) with 15 relapsed individuals identified. Maintenance chemotherapy is identified as a strong predictor of relapse, with individuals receiving high doses of cyclophosphamide or ifosphamide having only one very late molecularly confirmed relapse (p = 0.032). The anatomical location of recurrence is metastatic in 12 of 15 relapses, with 8 of 12 metastatic relapses in the lateral ventricles. Maintenance chemotherapy, specifically cumulative cyclophosphamide doses, is a significant predictor of relapse across WNT MB. Future efforts to de-escalate therapy need to carefully consider not only the radiation dose but also the chemotherapy regimen and the propensity for metastatic relapses