Beaufort Gyre Freshwater Experiment : deployment operations and technology 2003

The Beaufort Gyre Freshwater Experiment (BGFE) observational program was designed to measure the freshwater content of the upper ocean and sea ice in the Beaufort Gyre of the Arctic Ocean using bottom-tethered moorings, drifting buoys, and hydrographic stations. The mooring program required the development of a safe and efficient deployment method by which the subsurface system could be deployed in waters surrounded by sea ice. This report documents the mooring procedure used to deploy the three BGFE moorings from the CCGS Louis S. St- Laurent, during the Joint Western Arctic Climate Study – 2003 (August 6 – September 7). The technical details of the instrumentation attached to each mooring and the specific deployment parameters are described. Specifics pertaining to the deployment of four surface-tethered drifters in the ice are also documented.Funding was provided by the National Science Foundation under Grant Number OPP-0230184

The Beaufort Gyre Observing System 2004 : mooring recovery and deployment operations in pack ice

Situated beneath the Arctic perennial ice pack, the principal components of the Beaufort Gyre Observing System are three deep-ocean bottom-tethered moorings with CTD and velocity profilers, upward looking sonars for ice draft measurements, and bottom pressure recorders. A major goal of this project is to investigate basin-scale mechanisms regulating freshwater and heat content in the Arctic Ocean and particularly in the Beaufort Gyre throughout several complete annual cycles. The methods of recovering and re-deploying the 3800 m long instrumented moorings from the Canadian Coast Guard Icebreaker Louis S. St. Laurent in August 2004 are described. In ice-covered regions, deployments must be conducted anchor-first, so heavier wire rope and hardware must be incorporated into the mooring design. Backup buoyancy at the bottom of the mooring is advised for backup recovery should intermediate lengths of the mooring system get tangled under ice floes during recovery. An accurate acoustic survey to determine the exact location of the mooring, adequate ice conditions, and skilled ship maneuvering are all essential requirements for a successful mooring recovery. Windlass (or capstan) procedures could be used for the recovery, but a traction winch arrangement is recommended.Funding was provided by the National Science Foundation under Grant Number OPP-0230184 and Woods Hole Oceanographic Insitution’s Ocean and Climate Change Institute

1RXS J232953.9+062814: A Dwarf Nova with a 64-minute Orbital Period and a Conspicuous Secondary Star

We present spectroscopy and time-series photometry of the newly discovered dwarf nova 1RXS J232953.9+062814. Photometry in superoutburst reveals a superhump with a period of 66.06(6) minutes. The low state spectrum shows Balmer and HeI emission on a blue continuum, and in addition shows a rich absorption spectrum of type K4 +- 2. The absorption velocity is modulated sinusoidally at P_orb = 64.176(5) min, with semi-amplitude K = 348(4) km/s. The low-state light curve is double-humped at this period, and phased as expected for ellipsoidal variations. The absorption strength does not vary appreciably around the orbit. The orbital period is shorter than any other cataclysmic variable save for a handful of helium-star systems and V485 Centauri (59 minutes). The secondary is much hotter than main sequence stars of similar mass, but is well-matched by helium-enriched models, indicating that the secondary evolved from a more massive progenitor. A preliminary calculation in which a 1.2 solar-mass star begins mass transfer near the end of H burning matches this system's characteristics remarkably well.Comment: accepted to Astrophysical Journal Letters; 14 pages, 3 eps figures + 1 jpg greyscale figur

Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

As sequencing costs decrease and availability of high fidelity long-read sequencing increases, generating experiment specific de novo genome assemblies becomes feasible. In many crop species, obtaining the genome of a hybrid or heterozygous individual is necessary for systems that do not tolerate inbreeding or for investigating important biological questions, such as hybrid vigor. However, most genome assembly methods that have been used in plants result in a merged single sequence representation that is not a true biologically accurate representation of either haplotype within a diploid individual. The resulting genome assembly is often fragmented and exhibits a mosaic of the two haplotypes, referred to as haplotype-switching. Important haplotype level information, such as causal mutations and structural variation is therefore lost causing difficulties in interpreting downstream analyses. To overcome this challenge, we have applied a method developed for animal genome assembly called trio-binning to an intra-specific hybrid of chili pepper (Capsicum annuum L. cv. HDA149 x Capsicum annuum L. cv. HDA330). We tested all currently available softwares for performing trio-binning, combined with multiple scaffolding technologies including Bionano to determine the optimal method of producing the best haplotype-resolved assembly. Ultimately, we produced highly contiguous biologically true haplotype-resolved genome assemblies for each parent, with scaffold N50s of 266.0 Mb and 281.3 Mb, with 99.6% and 99.8% positioned into chromosomes respectively. The assemblies captured 3.10 Gb and 3.12 Gb of the estimated 3.5 Gb chili pepper genome size. These assemblies represent the complete genome structure of the intraspecific hybrid, as well as the two parental genomes, and show measurable improvements over the currently available reference genomes. Our manuscript provides a valuable guide on how to apply trio-binning to other plant genomes

Preliminary acoustic and oceanographic observations from the ASIAEX 2001 South China Sea Experiment

The Asian Seas International Experiment (ASIAEX) was a very successful scientific collaboration between the United States of America (USA), the People’s Republic of China (PRC), Taiwan (ROC), the Republic of Korea (ROK), Japan, Russia, and Singapore. Preliminary field experiments associated with ASIAEX began in spring of 2000. The main experiments were performed in April-August, 2001. The scientific plan called for two major acoustics experiments, the first a bottom interaction experiment in the East China Sea (ECS) and the second a volume interaction experiment in the South China Sea (SCS). In addition to the acoustics efforts, there were also extremely strong physical oceanography and geology and geophysics components to the experiments. This report will concentrate on describing the moored component of the South China Sea portion of ASIAEX 2001 performed from the Taiwan Fisheries research vessel FR1 (Fisheries Researcher 1). Information on the environmental moorings deployed from the Taiwanese oceanographic research vessel OR1 (Oceanographic Researcher 1) will also be listed here for completeness, so that the reader can pursue later analyses of the data. This report does not pursue any data analyses per se.Funding was provided by the Office of Naval Research under Grant Numbers N00014-01-1-0772, N00014-98-1-0413 and N00014-00-1-0206

The immune checkpoint CD96 defines a distinct lymphocyte phenotype and is highly expressed on tumor-infiltrating T cells

CD96 has recently been shown to be a potent immune checkpoint molecule in mice, but a similar role in humans is not known. In this study, we provide a detailed map of CD96 expression across human lymphocyte lineages, the kinetics of CD96 regulation on T-cell activation and co-expression with other conventional and emerging immune checkpoint molecules. We show that CD96 is predominantly expressed by T cells and has a unique lymphocyte expression profile. CD96 high T cells exhibited distinct effector functions on activation. Of note, CD96 expression was highly correlated with T-cell markers in primary and metastatic human tumors and was elevated on antigen- experienced T cells and tumor-infiltrating lymphocytes. Collectively, these data demonstrate that CD96 may be a promising immune checkpoint to enhance T-cell function against human cancer and infectious diseas

Highly efficient catalysis of the Kemp elimination in the cavity of a cubic coordination cage.

The hollow cavities of coordination cages can provide an environment for enzyme-like catalytic reactions of small-molecule guests. Here, we report a new example (catalysis of the Kemp elimination reaction of benzisoxazole with hydroxide to form 2-cyanophenolate) in the cavity of a water-soluble M8L12 coordination cage, with two features of particular interest. First, the rate enhancement is among the largest observed to date: at pD 8.5, the value of kcat/kuncat is 2 × 10(5), due to the accumulation of a high concentration of partially desolvated hydroxide ions around the bound guest arising from ion-pairing with the 16+ cage. Second, the catalysis is based on two orthogonal interactions: (1) hydrophobic binding of benzisoxazole in the cavity and (2) polar binding of hydroxide ions to sites on the cage surface, both of which were established by competition experiments

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