Velocity Analysis of Multi-Receiver Full Waveform Acoustic Logging Data In Open and Cased Holes

Average semblance and maximum-likelihood spectral analyses are applied to synthetic and field full waveform acoustic logging data to determine formation velocities. Of particular interest is the ability of these methods to resolve the P and shear/pseudo Rayleigh arrivals in data from poorly-bonded cased boreholes. In synthetic open-hole data the velocity analyses yield results within 4% of the true velocities. Results from synthetic well-bonded cased hole data are generally as good as those from the open hole data. However, if the formation P-wave velocity is within roughly 10% of the plate velocity of the steel pipe (about 5.3-5.5 km/s), then there may be a resonance effect that appears to slow down the P wave slightly (on the order of 6%). For cased-hole models with no steel/cement bonding (the free-pipe situation), the measured P-wave velocities are typically 6 to 8% less than the actual formation velocities. If the formation S-wave velocity is greater than about 2.5 km/s, the S-wave velocity estimate may also be 6 to 8% low. Furthermore, increasing the thickness of either the cement layer or the fluid layer between the pipe and the cement further decreases the formation velocity estimates. Also, if the P-wave velocity is within roughly 15% of the velocity of the steel arrival, the P wave may not be resolved by the semblance method unless the data is first low-pass filtered. Initial tests show that this filtering process may adversely affect the final P-wave velocity estimate, but the details of this type of approach have not been studied. The P wave is resolved. by spectral analysis of the original, unfiltered data. For cased-hole models with no cement/formation bonding (the unbonded-casing situation), formation S-wave velocities are estimated to within 3% relative error, and the formation P-wave velocity is estimated to within 2% error in a slow formation. However, for P-wave velocities between 3.4 km/s and 5.94 km/a, the P wave cannot be resolved by spectral analysis, and it is resolved by the semblance method only in the model with the low velocity (3.4 km/s).Massachusetts Institute of Technology. Full Waveform Acoustic Logging ConsortiumPhillips Petroleum Fellowshi

Digital Signal Processing

Contains summary of research and reports on sixteen research projects.U.S. Navy - Office of Naval Research (Contract N00014-75-C-0852)National Science Foundation FellowshipNATO FellowshipU.S. Navy - Office of Naval Research (Contract N00014-75-C-0951)National Science Foundation (Grant ECS79-15226)U.S. Navy - Office of Naval Research (Contract N00014-77-C-0257)Bell LaboratoriesNational Science Foundation (Grant ECS80-07102)Schlumberger-Doll Research Center FellowshipHertz Foundation FellowshipGovernment of Pakistan ScholarshipU.S. Navy - Office of Naval Research (Contract N00014-77-C-0196)U.S. Air Force (Contract F19628-81-C-0002)Hughes Aircraft Company Fellowshi

Digital Signal Processing

Contains an introduction and reports on seventeen research projects.U.S. Navy - Office of Naval Research (Contract N00014-77-C-0266)Amoco Foundation FellowshipU.S. Navy - Office of Naval Research (Contract N00014-81-K-0742)National Science Foundation (Grant ECS80-07102)U.S. Army Research Office (Contract DAAG29-81-K-0073)Hughes Aircraft Company FellowshipAmerican Edwards Labs. GrantWhitaker Health Sciences FundPfeiffer Foundation GrantSchlumberger-Doll Research Center FellowshipGovernment of Pakistan ScholarshipU.S. Navy - Office of Naval Research (Contract N00014-77-C-0196)National Science Foundation (Grant ECS79-15226)Hertz Foundation Fellowshi

Digital Signal Processing

Contains research objectives and reports on sixteen research projects.U.S. Navy - Office of Naval Research (Contract N00014-75-C-0852)National Science Foundation FellowshipNational Science Foundation (Grant ENG76-24117)U.S. Navy - Office of Naval Research (Contract N00014-77-C-0257)U.S. Air Force (Contract F19628-80-C-0002)U.S. Navy - Office of Naval Research (Contract N00014-75-C-0951)Schlumberger-Doll Research Center FellowshipHertz Foundation FellowshipGovernment of Pakistan ScholarshipU.S. Navy - Office of Naval Research (Contract N00014-77-C-0196

Digital Signal Processing

Contains a research summary and reports on fifteen research projects.National Science Foundation FellowshipJoint Services Electronics Program (Contract DAAG29-78-C-0020)National Science Foundation (Grant ENG76-24117)U.S. Navy - Office of Naval Research (Contract N00014-75-C-0951)National Science Foundation (Grant ENG76-24117)Schlumberger-Doll Research Center FellowshipHertz Foundation FellowshipNational Aeronautics and Space Administration (Grant NSG-5157)U.S. Navy - Office of Naval Research (Contract N00014-77-C-0196

Digital Signal Processing Group

Contains an introduction and reports on nineteen research projects.U.S. Navy - Office of Naval Research (Contract N00014-77-C-0266)U.S. Navy - Office of Naval Research (Contract N00014-81-K-0742)National Science Foundation (Grant ECS80-07102)Bell Laboratories FellowshipAmoco Foundation FellowshipU.S. Navy - Office of Naval Research (Contract N00014-77-C-0196)Schlumberger-Doll Research Center FellowshipToshiba Company FellowshipVinton Hayes FellowshipHertz Foundation Fellowshi

Conscious uncoupling between FANCI and FANCD2 in DNA repair

The Fanconi anemia (FA)-BRCA pathway mediates repair of DNA interstrand crosslinks. The FA core complex, a multi-subunit ubiquitin ligase, participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins, FANCD2 and FANCI (or the ID complex). However, the regulation of the FA core complex itself is poorly understood. Here we show that the FA core complex proteins are recruited to sites of DNA damage and form nuclear foci in S and G2 phases of the cell cycle. ATR kinase activity, an intact FA core complex and FANCM-FAAP24 were crucial for this recruitment. Surprisingly, FANCI, but not its partner FANCD2, was needed for efficient FA core complex foci formation. Monoubiquitination or ATR-dependent phosphorylation of FANCI were not required for the FA core complex recruitment, but FANCI deubiquitination by USP1 was. Additionally, BRCA1 was required for efficient FA core complex foci formation. These findings indicate that FANCI functions upstream of FA core complex recruitment independently of FANCD2, and alter the current view of the FA-BRCA pathway

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.This work is supported by the UK Medical Research Council (MRC); Chinese Academy of Medical Sciences(CAMS) Innovation Fund for Medical Sciences (CIFMS), China; National Institute for Health Research (NIHR)Oxford Biomedical Research Centre, and UK Researchand Innovation (UKRI)/NIHR through the UK Coro-navirus Immunology Consortium (UK-CIC). Sequencing of SARS-CoV-2 samples and collation of data wasundertaken by the COG-UK CONSORTIUM. COG-UK is supported by funding from the Medical ResearchCouncil (MRC) part of UK Research & Innovation (UKRI),the National Institute of Health Research (NIHR),and Genome Research Limited, operating as the Wellcome Sanger Institute. T.I.d.S. is supported by a Well-come Trust Intermediate Clinical Fellowship (110058/Z/15/Z). L.T. is supported by the Wellcome Trust(grant number 205228/Z/16/Z) and by theUniversity of Liverpool Centre for Excellence in Infectious DiseaseResearch (CEIDR). S.D. is funded by an NIHR GlobalResearch Professorship (NIHR300791). L.T. and S.C.M.are also supported by the U.S. Food and Drug Administration Medical Countermeasures Initiative contract75F40120C00085 and the National Institute for Health Research Health Protection Research Unit (HPRU) inEmerging and Zoonotic Infections (NIHR200907) at University of Liverpool inpartnership with Public HealthEngland (PHE), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford.L.T. is based at the University of Liverpool. M.D.P. is funded by the NIHR Sheffield Biomedical ResearchCentre (BRC – IS-BRC-1215-20017). ISARIC4C is supported by the MRC (grant no MC_PC_19059). J.C.K.is a Wellcome Investigator (WT204969/Z/16/Z) and supported by NIHR Oxford Biomedical Research Centreand CIFMS. The views expressed are those of the authors and not necessarily those of the NIHR or MRC

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant