Analysis & experimental evaluation of single point moored buoy systems

Originally issued as Reference No. 69-36, series later renamed WHOI-This report reviews the analysis and the evaluation of surface buoy systems performed in the Engineering Department of the Woods Hole Oceanographic Institution in 1968. The buoy systems considered are single point moored, taut and compound consisting of wire and synthetic ropes, The first part of the report describes the forcing functions and the system response as measured in situ during and after launching, The second part presents the results of the mooring line components testing and evaluation programs performed at sea or in laboratories. The third part briefly outlines the present development in telemetry transmission of scientific and engineering information, It is believed that this systematic engineering effort is an important factor in the continuous improvement of the reliability and performance of the deep sea buoy systems used in scientific measurements programs.Submitted to the Office of Naval Research under Contract N00014-66-C0241, NR 083-00

Design of a stable floating platform for air-sea interaction measurements

The design of an oceanographic platform can be defined as the rational specification of the platform dimensions and geometry. This specification is usually the result of an iterative process which compares the platform performance with the objectives to be reached and the logistic constraints to be met. This report describes such an exercise. The scientific objectives - measurements of heat flux at the ocean surface - are first outlined. The limits of heave and roll motion compatible with the desired measurement accuracy are then established. Given the stochastic nature of platform response, these limits are stipulated in terms of expected means. A review is then made, in some detail, of the analytical approach followed and of the computer programs used to compute the statistical expectations of buoy heave and roll response to random sea excitation. The next section of the report describes the comprehensive parametric study performed on some twenty different buoy configurations. The purpose of this study was first to investigate the dynamic response of a plausible base line design and of modified versions of the base line. A comparison of the dynamic response of these configurations could then"be made, and the good features that this comparison would reveal could be used to design the buoy prototype. Following this approach a final configuration was specified which would meet the rather severe motion requirements (0. 2 feet RMS in heave and 5. 0 degrees RMS in roll in sea state 3). The final section describes the techniques recommended to deploy and recover the 60 feet long buoy prototype.Prepared for the Johns Hopkins University, Applied Physics Laboratory under Subcontract 600651

Self deployable deep sea moorings

As part of a development effort in the field of moored arrays sponsored by the Office of Naval Technology, the Ocean Structures and Moorings Laboratory (OSM&L), Applied Ocean Physics and Engineering Department (AOP&E), Woods Hole Oceanographic Institution (WHOI) conducted a study in 1991 to assess the feasibility and the merits of several self-deployable mooring designs. This study included a brief review of the state of the art, the performance of lab tests to evaluate different mooring line payout concepts, and the preliminary design of a typical candidate mooring. The results of this study are presented in this report. The report first reviews three types of single point moored arrays which are amenable to self-deployment: subsurface, subsurface with surface expression, and surface with bottom inverted catenary. It then describes the features common to all self-deploying moorings: techniques for line and instrument storage, means for controlled payout, bottom finders and lock up mechanisms, and it also outlines desirable specifications for sensor sizes, cables and connectors. Next the report reviews typical deployment scenarios from the bottom up or from the surface down as they apply to the three types of moorings retained. In its final section, the report presents the conceptual design of a 6000 meters depth capability, bottom up deployment, candidate mooring. This configuration should be of strong interest when contemplating the deployment of a large number of identical subsurface moorings, interconnected by a bottom cable, and in "close" proximity to one another. The case study outlines the design objectives and the current profiles, specifies the main components, evaluates their performance with the help of a standard computer program, and presents packaging and payout control details. Finally, a plan is proposed for the controlled, in-situ evaluation of a prototype.Funding was provided by the Office of Naval Technology under Contract No. N00014-90-C-0098

A study of CTD cables and lowering systems

This study first reviews both the electrical and mechanical modes and causes of failure of electromechanical (E/M) cables used to lower deep sea sensors, such as CTD instruments, from oceanographic ships. It then outlines measures or steps that could be taken to correct some of the deficiencies observed and improve the systems presently used. These measures include quality control, tests, operational limits, improved handling and maintenance, improved machinery. The study then surveys alternative cables for lowering the sensors and convey the information from the sensors back to the ship. These alternatives include strength members other than steel (Kevlar)and signal carriers other than conventional copper conductors (fiber optics). The final section - Conclusions - summarizes the recommendations, based on this study, for improving the reliability of present and future CTD lowering systems.Prepared for the Office of Naval Research under Contract N00014-7l6-C-0197; NR 083-400

Experimental evaluation of CTD package hydrodynamic behavior and recommendations for improved lowering techniques

This report is the last of a series of three reports on a comprehensive study of CTD instrument lowering mechanics. The first report, WHOI 79-81, "A Study of CTD Cables and Lowering Systems", examines the causes and modes of lowering cable failures, both mechanical and electrical, and makes recommendations to improve existing instrument packages and lowering procedures. The second report, WHOI 81-76, "Hydrodynamics of CTD Instrument Packages", is a theoretical study of instrument package stability when cable lowered or free falling. The model is used to predict the hydrodynamic response of CTD packages in their present or improved configuration. This report, WHOI 83-21, is more factual. It describes the tests performed on scale models and actual CTD packages to actually observe and/or measure their hydrodynamic behavior. Analytical results and experimental data obtained in this study are used to draw recommendations for CTD package improvement and future lowering procedures.Prepared for the Office of Naval Research under Contract N00014-72-C-0019

Performance analysis of Woods Hole taut moorings

The Woods Hole Oceanographic Institution has been using deepsea moored buoys for acquiring serial observations of ocean currents, temperature .and other data for over twelve years. A brief description of the deep-sea mooring program is given. The mooring statistics and performance are described. Mooring failures of 1970 and 1971 have been categorized and statistics on the modes and causes of failures are presented. The reliabilities of different types of moorings are computed and compared. The role of radio telemetry for the real-time measurement of mooring line tension and its use in checking the mooring status are discussed. Examples of potential design data like tension and currents recorded by moorings that failed are provided. Finally, recommendations for research and development needed to improve mooring reliability are given.Prepared for the Office of NavaZ Research under Contract N00014-66-C024lj NR 083-004

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine learning, and causal analyses are most successful with large-scale data beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient-level data from many centers. MATERIALS AND METHODS: The Clinical and Translational Science Award Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level clinical data. We developed solutions to extract, aggregate, and harmonize data across organizations and data models, and created a secure data enclave to enable efficient, transparent, and reproducible collaborative analytics. RESULTS: Organized in inclusive workstreams, we created legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible COVID-19 cases; a data quality assurance and harmonization pipeline to create a single harmonized dataset; population of the secure data enclave with data, machine learning, and statistical analytics tools; dissemination mechanisms; and a synthetic data pilot to democratize data access. CONCLUSIONS: The N3C has demonstrated that a multisite collaborative learning health network can overcome barriers to rapidly build a scalable infrastructure incorporating multiorganizational clinical data for COVID-19 analytics. We expect this effort to save lives by enabling rapid collaboration among clinicians, researchers, and data scientists to identify treatments and specialized care and thereby reduce the immediate and long-term impacts of COVID-19

The CCP4 suite: integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.Jon Agirre is a Royal Society University Research Fellow (UF160039 and URF\R\221006). Mihaela Atanasova is funded by the UK Engineering and Physical Sciences Research Council (EPSRC; EP/R513386/1). Haroldas Bagdonas is funded by The Royal Society (RGF/R1/181006). Jose´ Javier Burgos-Ma´rmol and Daniel J. Rigden are supported by the BBSRC (BB/S007105/1). Robbie P. Joosten is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 871037 (iNEXTDiscovery) and by CCP4. This work was supported by the Medical Research Council as part of United Kingdom Research and Innovation, also known as UK Research and Innovation: MRC file reference No. MC_UP_A025_1012 to Garib N. Murshudov, which also funded Keitaro Yamashita, Paul Emsley and Fei Long. Robert A. Nicholls is funded by the BBSRC (BB/S007083/1). Soon Wen Hoh is funded by the BBSRC (BB/T012935/1). Kevin D. Cowtan and Paul S. Bond are funded in part by the BBSRC (BB/S005099/1). John Berrisford and Sameer Velankar thank the European Molecular Biology Laboratory–European Bioinformatics Institute, who supported this work. Andrea Thorn was supported in the development of AUSPEX by the German Federal Ministry of Education and Research (05K19WWA and 05K22GU5) and by Deutsche Forschungsgemeinschaft (TH2135/2-1). Petr Kolenko and Martin Maly´ are funded by the MEYS CR (CZ.02.1.01/0.0/0.0/16_019/0000778). Martin Maly´ is funded by the Czech Academy of Sciences (86652036) and CCP4/STFC (521862101). Anastassis Perrakis acknowledges funding from iNEXT (grant No. 653706), iNEXT-Discovery (grant No. 871037), West-Life (grant No. 675858) and EOSC-Life (grant No. 824087) funded by the Horizon 2020 program of the European Commission. Robbie P. Joosten has been the recipient of a Veni grant (722.011.011) and a Vidi grant (723.013.003) from the Netherlands Organization for Scientific Research (NWO). Maarten L. Hekkelman, Robbie P. Joosten and Anastassis Perrakis thank the Research High Performance Computing facility of the Netherlands Cancer Institute for providing and maintaining computation resources and acknowledge the institutional grant from the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. Tarik R. Drevon is funded by the BBSRC (BB/S007040/1). Randy J. Read is supported by a Principal Research Fellowship from the Wellcome Trust (grant 209407/Z/17/Z). Atlanta G. Cook is supported by a Wellcome Trust SRF (200898) and a Wellcome Centre for Cell Biology core grant (203149). Isabel Uso´n acknowledges support from STFC-UK/CCP4: ‘Agreement for the integration of methods into the CCP4 software distribution, ARCIMBOLDO_LOW’ and Spanish MICINN/AEI/FEDER/UE (PID2021-128751NB-I00). Pavol Skubak and Navraj Pannu were funded by the NWO Applied Sciences and Engineering Domain and CCP4 (grant Nos. 13337 and 16219). Bernhard Lohkamp was supported by the Ro¨ntgen A˚ ngstro¨m Cluster (grant 349-2013-597). Nicholas Pearce is currently funded by the SciLifeLab and Wallenberg Data Driven Life Science Program (grant KAW 2020.0239) and has previously been funded by a Veni Fellowship (VI.Veni.192.143) from the Dutch Research Council (NWO), a Long-term EMBO fellowship (ALTF 609-2017) and EPSRC grant EP/G037280/1. David M. Lawson received funding from BBSRC Institute Strategic Programme Grants (BB/P012523/1 and BB/P012574/1). Lucrezia Catapano is the recipient of an STFC/CCP4-funded PhD studentship (Agreement No: 7920 S2 2020 007).Peer reviewe

Phylogenomics and the evolution of hemipteroid insects.

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group