Tools for Atmospheric Radiative Transfer: Streamer and FluxNet

Two tools for the solution of radiative transfer problems are presented. Streamer is a highly flexible medium spectral resolution radiative transfer model based on the plane-parallel theory of radiative transfer. Capable of computing either fluxes or radiances, it is suitable for studying radiative processes at the surface or within the atmosphere and for the development of remote-sensing algorithms. FluxNet is a fast neural network-based implementation of Streamer for computing surface fluxes. It allows for a sophisticated treatment of radiative processes in the analysis of large data sets and potential integration into geophysical models where computational efficiency is an issue. Documentation and tools for the development of alternative versions of Fluxnet are available. Collectively, Streamer and FluxNet solve a wide variety of problems related to radiative transfer: Streamer provides the detail and sophistication needed to perform basic research on most aspects of complex radiative processes while the efficiency and simplicity of FluxNet make it ideal for operational use

Biophysical consequences of a relaxing Beaufort Gyre

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, J., Spitz, Y. H., Steele, M., Ashjian, C., Campbell, R., & Schweiger, A. Biophysical consequences of a relaxing Beaufort Gyre. Geophysical Research Letters, 47(2), (2020): e2019GL085990, doi:10.1029/2019GL085990.A biophysical model shows that Beaufort Gyre (BG) intensification in 2004–2016 is followed by relaxation in 2017–2018, based on a BG variability index. BG intensification leads to enhanced downwelling in the central Canada Basin (CCB) and upwelling along the coast. In the CCB, enhanced downwelling reduces nutrients, thus lowering primary productivity (PP) and plankton biomass. Enhanced upwelling along the coast and in parts of the Chukchi shelf/slope increases nutrients, leading to elevated PP/biomass in the Pacific Arctic Ocean (PAO) outside of the CCB. The overall PAO PP/biomass is dominated by the shelf/slope response and thus increases during BG intensification. As the BG relaxes in 2017–2018, these processes largely reverse, with increasing PP/biomass in the CCB and decreasing PP/biomass in most of the shelf/slope regions. Because the shelf/slope regions are much more productive than the CCB, BG relaxation has the tendency to reduce the overall production in the PAO.This work is funded by the NASA Cryosphere Program (NNX15AG68G and NNX17AD27G), the NSF Office of Polar Programs (PLR‐1416920, PLR‐1603259, PLR‐1603266, OPP‐1751363, PLR‐1602521, and PLR‐1503298), the NOAA Climate Program Office (NA15OAR4310170 and NA15OAR4320063AM170), and ONR (N00014‐17‐1‐2545). We thank Drs. Benjamin Rabe and Edward Doddridge for their constructive comments and Kay Runciman for graphics support. CFS reanalysis data used for model forcing are available online (https://www.ncdc.noaa.gov/data‐access/model‐data/model‐datasets/climate‐forecast‐system‐version2‐cfsv2). Model results are in https://pscfiles.apl.uw.edu/zhang/BIOMAS168x180/ website

Melt pond conditions on declining arctic sea ice over 1979-2016: Model development, validation, and results

Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Oceans, 123(11), (2018): 7983-8003. doi:10.1029/2018JC014298.A melt pond (MP) distribution equation has been developed and incorporated into the Marginal Ice‐Zone Modeling and Assimilation System to simulate Arctic MPs and sea ice over 1979–2016. The equation differs from previous MP models and yet benefits from previous studies for MP parameterizations as well as a range of observations for model calibration. Model results show higher magnitude of MP volume per unit ice area and area fraction in most of the Canada Basin and the East Siberian Sea and lower magnitude in the central Arctic. This is consistent with Moderate Resolution Imaging Spectroradiometer observations, evaluated with Measurements of Earth Data for Environmental Analysis (MEDEA) data, and closely related to top ice melt per unit ice area. The model simulates a decrease in the total Arctic sea ice volume and area, owing to a strong increase in bottom and lateral ice melt. The sea ice decline leads to a strong decrease in the total MP volume and area. However, the Arctic‐averaged MP volume per unit ice area and area fraction show weak, statistically insignificant downward trends, which is linked to the fact that MP water drainage per unit ice area is increasing. It is also linked to the fact that MP volume and area decrease relatively faster than ice area. This suggests that overall the actual MP conditions on ice have changed little in the past decades as the ice cover is retreating in response to Arctic warming, thus consistent with the Moderate Resolution Imaging Spectroradiometer observations that show no clear trend in MP area fraction over 2000–2011.We gratefully acknowledge the support of the NASA Cryosphere Program (grants NNX15AG68G, NNX17AD27G, and NNX14AH61G), the Office of Naval Research (N00014‐12‐1‐0112), the NSF Office of Polar Programs (PLR‐1416920, PLR‐1603259, PLR‐1602521, and ARC‐1203425), and the Department of Homeland Security (DHS, 2014‐ST‐061‐ML‐0002). The DHS grant is coordinated through the Arctic Domain Awareness Center (ADAC), a DHS Center of Excellence, which conducts maritime research and development for the Arctic region. The views and conclusions in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the DHS. MODIS‐derived MP area data are available at https://icdc.cen.uni‐hamburg.de/1/daten/cryosphere/arctic‐meltponds.html. MP area fraction statistics derived from MEDEA images are available from http://psc.apl.uw.edu/melt‐pond‐data/. Sea ice thickness and snow observations are available at http://psc.apl.washington.edu/sea_ice_cdr. CFS forcing data used to drive MIZMAS are available at https://www.ncdc.noaa.gov/data‐access/model‐data/model‐datasets/climate‐forecast‐system‐version2‐cfsv2.2019-04-1

Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics

<p>Abstract</p> <p>Background</p> <p>The heat shock protein 90 (Hsp90) is required for the stability of many signalling kinases. As a target for cancer therapy it allows the simultaneous inhibition of several signalling pathways. However, its inhibition in healthy cells could also lead to severe side effects. This is the first comprehensive analysis of the response to Hsp90 inhibition at the kinome level.</p> <p>Methods</p> <p>We quantitatively profiled the effects of Hsp90 inhibition by geldanamycin on the kinome of one primary (Hs68) and three tumour cell lines (SW480, U2OS, A549) by affinity proteomics based on immobilized broad spectrum kinase inhibitors ("kinobeads"). To identify affected pathways we used the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway classification. We combined Hsp90 and proteasome inhibition to identify Hsp90 substrates in Hs68 and SW480 cells. The mutational status of kinases from the used cell lines was determined using next-generation sequencing. A mutation of Hsp90 candidate client RIPK2 was mapped onto its structure.</p> <p>Results</p> <p>We measured relative abundances of > 140 protein kinases from the four cell lines in response to geldanamycin treatment and identified many new potential Hsp90 substrates. These kinases represent diverse families and cellular functions, with a strong representation of pathways involved in tumour progression like the BMP, MAPK and TGF-beta signalling cascades. Co-treatment with the proteasome inhibitor MG132 enabled us to classify 64 kinases as true Hsp90 clients. Finally, mutations in 7 kinases correlate with an altered response to Hsp90 inhibition. Structural modelling of the candidate client RIPK2 suggests an impact of the mutation on a proposed Hsp90 binding domain.</p> <p>Conclusions</p> <p>We propose a high confidence list of Hsp90 kinase clients, which provides new opportunities for targeted and combinatorial cancer treatment and diagnostic applications.</p

Predicting September Arctic Sea Ice: A Multi-Model Seasonal Skill Comparison

Abstract This study quantifies the state-of-the-art in the rapidly growing field of seasonal Arctic sea ice prediction. A novel multi-model dataset of retrospective seasonal predictions of September Arctic sea ice is created and analyzed, consisting of community contributions from 17 statistical models and 17 dynamical models. Prediction skill is compared over the period 2001–2020 for predictions of Pan-Arctic sea ice extent (SIE), regional SIE, and local sea ice concentration (SIC) initialized on June 1, July 1, August 1, and September 1. This diverse set of statistical and dynamical models can individually predict linearly detrended Pan-Arctic SIE anomalies with skill, and a multi-model median prediction has correlation coefficients of 0.79, 0.86, 0.92, and 0.99 at these respective initialization times. Regional SIE predictions have similar skill to Pan-Arctic predictions in the Alaskan and Siberian regions, whereas regional skill is lower in the Canadian, Atlantic, and Central Arctic sectors. The skill of dynamical and statistical models is generally comparable for Pan-Arctic SIE, whereas dynamical models outperform their statistical counterparts for regional and local predictions. The prediction systems are found to provide the most value added relative to basic reference forecasts in the extreme SIE years of 1996, 2007, and 2012. SIE prediction errors do not show clear trends over time, suggesting that there has been minimal change in inherent sea ice predictability over the satellite era. Overall, this study demonstrates that there are bright prospects for skillful operational predictions of September sea ice at least three months in advance.</jats:p

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Combined searches for the production of supersymmetric top quark partners in proton-proton collisions at root s=13 TeV

A combination of searches for top squark pair production using proton-proton collision data at a center-of-mass energy of 13 TeV at the CERN LHC, corresponding to an integrated luminosity of 137 fb(-1) collected by the CMS experiment, is presented. Signatures with at least 2 jets and large missing transverse momentum are categorized into events with 0, 1, or 2 leptons. New results for regions of parameter space where the kinematical properties of top squark pair production and top quark pair production are very similar are presented. Depending on themodel, the combined result excludes a top squarkmass up to 1325 GeV for amassless neutralino, and a neutralinomass up to 700 GeV for a top squarkmass of 1150 GeV. Top squarks with masses from 145 to 295 GeV, for neutralino masses from 0 to 100 GeV, with a mass difference between the top squark and the neutralino in a window of 30 GeV around the mass of the top quark, are excluded for the first time with CMS data. The results of theses searches are also interpreted in an alternative signal model of dark matter production via a spin-0 mediator in association with a top quark pair. Upper limits are set on the cross section for mediator particle masses of up to 420 GeV

Development and validation of HERWIG 7 tunes from CMS underlying-event measurements

This paper presents new sets of parameters (“tunes”) for the underlying-event model of the HERWIG7 event generator. These parameters control the description of multiple-parton interactions (MPI) and colour reconnection in HERWIG7, and are obtained from a fit to minimum-bias data collected by the CMS experiment at s=0.9, 7, and 13Te. The tunes are based on the NNPDF 3.1 next-to-next-to-leading-order parton distribution function (PDF) set for the parton shower, and either a leading-order or next-to-next-to-leading-order PDF set for the simulation of MPI and the beam remnants. Predictions utilizing the tunes are produced for event shape observables in electron-positron collisions, and for minimum-bias, inclusive jet, top quark pair, and Z and W boson events in proton-proton collisions, and are compared with data. Each of the new tunes describes the data at a reasonable level, and the tunes using a leading-order PDF for the simulation of MPI provide the best description of the dat

Search for new particles in events with energetic jets and large missing transverse momentum in proton-proton collisions at root s=13 TeV

A search is presented for new particles produced at the LHC in proton-proton collisions at root s = 13 TeV, using events with energetic jets and large missing transverse momentum. The analysis is based on a data sample corresponding to an integrated luminosity of 101 fb(-1), collected in 2017-2018 with the CMS detector. Machine learning techniques are used to define separate categories for events with narrow jets from initial-state radiation and events with large-radius jets consistent with a hadronic decay of a W or Z boson. A statistical combination is made with an earlier search based on a data sample of 36 fb(-1), collected in 2016. No significant excess of events is observed with respect to the standard model background expectation determined from control samples in data. The results are interpreted in terms of limits on the branching fraction of an invisible decay of the Higgs boson, as well as constraints on simplified models of dark matter, on first-generation scalar leptoquarks decaying to quarks and neutrinos, and on models with large extra dimensions. Several of the new limits, specifically for spin-1 dark matter mediators, pseudoscalar mediators, colored mediators, and leptoquarks, are the most restrictive to date.Peer reviewe

Probing effective field theory operators in the associated production of top quarks with a Z boson in multilepton final states at root s=13 TeV

Peer reviewe