New England Cod Collapse and the Climate.

To improve fishery management, there is an increasing need to understand the long-term consequences of natural and anthropogenic climate variability for ecological systems. New England's iconic cod populations have been in decline for several decades and have recently reached unprecedented lows. We find that 17% of the overall decline in Gulf of Maine cod biomass since 1980 can be attributed to positive phases of the North Atlantic Oscillation (NAO). This is a consequence of three results: i) a 1-unit increase in the NAO winter index is associated with a 17% decrease in the spring biomass of age-1 cod the following year; ii) this NAO-driven decrease persists as the affected cohort matures; iii) fishing practices appear to exacerbate NAO's direct biological effect such that, since 1913, a 1-unit increase in the NAO index lowers subsequent cod catch for up to 19 years. The Georges Bank cod stock displays similar patterns. Because we statistically detect a delay between the NAO and subsequent declines in adult biomass, our findings imply that observed current NAO conditions can be used in stock forecasts, providing lead time for adaptive policy. More broadly, our approach can inform forecasting efforts for other fish populations strongly affected by natural and anthropogenic climatic variation

Reply to Swartz et al.: Challenges and opportunities for identifying forced labor using satellite-based fishing vessel monitoring

We appreciate Swartz et al. (1) for highlighting several key considerations for interpreting our results (2). While we discuss many of these in our paper, we are grateful to further highlight our work’s strengths, limitations, and future opportunities. A major challenge with understanding fisheries labor abuses is a lack of data. Automatic identification system (AIS) is only used by a subset of the global fishing fleet. However, AIS is valuable for monitoring certain types of fishing vessels, especially those that are large (∼52 to 85% carry AIS) (3) and those fishing on the high seas (∼80% carry AIS) (4). Mandating AIS and unique identifiers on fishing vessels and publishing vessel registries would facilitate more inclusive AIS-based analyses (5)

Fast frequency response from energy storage systems - A review of grid standards, projects and technical issues

Electric power systems foresee challenges in stability due to the high penetration of power electronics interfaced renewable energy sources. The value of energy storage systems (ESS) to provide fast frequency response has been more and more recognized. Although the development of energy storage technologies has made ESSs technically feasible to be integrated in larger scale with required performance, the policies, grid codes and economic issues are still presenting barriers for wider application and investment. Recent years, a few regions and countries have designed new services to meet the upcoming grid challenges. A number of grid-scale ESS projects are also implemented aiming to trial performance, demonstrate values, and gain experience. This paper makes a review on the above mentioned aspects, including the emerging frequency regulation services, updated grid codes and grid-scale ESS projects. Some key technical issues are also discussed and prospects are outlined

Investigating the Lower Mass Gap with Low Mass X-ray Binary Population Synthesis

Mass measurements from low-mass black hole X-ray binaries (LMXBs) and radio pulsars have been used to identify a gap between the most massive neutron stars (NSs) and the least massive black holes (BHs). BH mass measurements in LMXBs are typically only possible for transient systems: outburst periods enable detection via all-sky X-ray monitors, while quiescent periods enable radial-velocity measurements of the low-mass donor. We quantitatively study selection biases due to the requirement of transient behavior for BH mass measurements. Using rapid population synthesis simulations (COSMIC), detailed binary stellar-evolution models (MESA), and the disk instability model of transient behavior, we demonstrate that transient-LMXB selection effects introduce observational biases, and can suppress mass-gap BHs in the observed sample. However, we find a population of transient LMXBs with mass-gap BHs form through accretion-induced collapse of a NS during the LMXB phase, which is inconsistent with observations. These results are robust against variations of binary evolution prescriptions. The significance of this accretion-induced collapse population depends upon the maximum NS birth mass $M_\mathrm{ NS, birth-max}$. To reflect the observed dearth of low-mass BHs, COSMIC and MESA models favor $M_\mathrm{ NS, birth-max} \lesssim2M_{\odot}$. In the absence of further observational biases against LMXBs with mass-gap BHs, our results indicate the need for additional physics connected to the modeling of LMXB formation and evolution.Comment: 21 pages, accepted to Ap

IFN-γ Rα Is a Key Determinant of CD8+ T Cell-Mediated Tumor Elimination or Tumor Escape and Relapse in FVB Mouse

During the past decade, the dual function of the immune system in tumor inhibition and tumor progression has become appreciated. We have previously reported that neu-specific T cells can induce rejection of neu positive mouse mammary carcinoma (MMC) and also facilitate tumor relapse by inducing neu antigen loss and epithelial to mesenchymal transition (EMT). Here, we sought to determine the mechanism by which CD8+ T cells either eliminate the tumor, or maintain tumor cells in a dormant state and eventually facilitate tumor relapse. We show that tumor cells that express high levels of IFN-γ Rα are eliminated by CD8+ T cells. In contrast, tumor cells that express low levels of IFN-γ Rα do not die but remain dormant and quiescent in the presence of IFN-γ producing CD8+ T cells until they hide themselves from the adaptive immune system by losing the tumor antigen, neu. Relapsed tumor cells show CD44+CD24- phenotype with higher rates of tumorigenesis, in vivo. Acquisition of CD44+CD24- phenotype in relapsed tumors was not solely due to Darwinian selection. Our data suggest that tumor cells control the outcome of tumor immune surveillance through modulation of the expression of IFN-γ Rα

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

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